CCDS55125.1	2018-04-17	The coding region has been updated to start at a downstream in-frame start codon that is more supported by conservation data
CCDS4790.1	2018-04-16	This coding region is updated to annotate a different coding sequence, which is shorter and reflects the use of an alternate start codon that is better supported by conservation and ribosome profiling. 
CCDS45233.1	2018-03-06	The coding region has been updated to trim the N-terminus to one that is more supported by available transcript data, CAGE data and conservation data. 
CCDS11552.2	2018-03-05	The coding region has been updated to scale back the N-terminus to one that is more supported by the available transcript data and by conservation across mammals.
CCDS44134.1	2018-03-05	The coding region has been updated to scale back the N-terminus to one that is more supported by the available transcript data and by conservation across mammals.
CCDS30705.1	2018-03-05	The coding region has been updated to scale back the N-terminus to one that is more supported by the available transcript data and by conservation across mammals.
CCDS538.1	2018-03-05	The coding region has been updated to scale back the N-terminus to one that is more supported by the available transcript data and by conservation across mammals.
CCDS72690.1	2018-02-14	The coding region has been updated to start at a downstream in-frame start codon that has better support from conservation data.
CCDS72691.1	2018-02-14	The coding region has been updated to start at a downstream in-frame start codon that has better support from conservation data.
CCDS55564.1	2018-02-14	The coding region has been updated to start at a downstream in-frame start codon that has better support from conservation data.
CCDS14097.2	2017-11-22	The coding region has been updated to start at an alternate in-frame start codon that is more supported by conservation data.
CCDS12300.1	2017-11-21	The coding region has been updated to start at an alternate in-frame start codon that is more supported by conservation data.  
CCDS34616.1	2017-11-17	The coding region has been updated to start at a downstream in-frame start codon that is more supported by conservation data.
CCDS34907.1	2017-11-17	The coding region has been updated to start at an alternate start codon and to represent an exon combination that is more supported by the available data. The earlier representation (NM_172059.3) was partial at the 5' end. 
CCDS33339.1	2017-11-17	The coding region has been updated to start at an alternate in-frame start codon that is more supported by conservation data.
CCDS34124.1	2017-11-16	The coding region has been updated to represent an exon combination that is more supported by available data. The earlier representation (NM_052909.3) was partial at the 5' end.
CCDS11363.1	2017-11-15	The coding region has been updated to start at an alternate in-frame start codon that is more supported by conservation data.
CCDS33881.1	2017-11-13	The coding region has been updated to start at an alternate start codon that is more supported by available transcripts and conservation data.
CCDS1053.1	2017-11-13	The coding region has been updated to start at an alternate in-frame start codon that is more supported by conservation data.
CCDS59242.1	2017-11-08	This CCDS ID represents the protein described in PMIDs: 12364586 and 14966479. This transcript is supported by AY170469.2. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 18544534. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein. 
CCDS45779.2	2016-11-28	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript data.
CCDS41561.1	2016-11-28	The coding region has been updated to add an additional glycine residue in the protein C-terminal region, supported by the available transcript and conservation data.
CCDS74631.1	2016-11-28	The coding region has been updated to represent an alternative protein C-terminus that is more supported by the available transcript data.  
CCDS56380.2	2016-11-28	The coding region has been updated to shorten the N-terminus based on the use of a downstream in-frame start codon, which is more supported by the available transcript and conservation data. There is a higher probability of an N-terminal transit peptide being present in the updated protein.
CCDS54426.2	2016-11-28	The coding region has been updated to shorten the N-terminus to one that is more supported by the available transcript and conservation data.
CCDS42872.2	2016-11-28	The coding region has been updated to shorten the N-terminus based on the use of a downstream in-frame start codon, which is supported by ribosome profiling and conservation data.
CCDS58398.1	2016-11-28	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript and conservation data.
CCDS4146.1	2016-11-28	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript and conservation data.
CCDS1232.1	2016-11-28	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript data and by conservation in primates.
CCDS47500.2	2016-09-08	
CCDS54780.1	2016-09-08	
CCDS46298.1	2016-09-08	
CCDS53929.1	2016-09-08	
CCDS44732.1	2016-09-08	
CCDS44704.1	2016-09-08	
CCDS43753.1	2016-09-08	
CCDS5289.1	2016-09-08	
CCDS5092.1	2016-09-08	
CCDS44636.1	2016-09-08	
CCDS35307.1	2016-08-19	
CCDS81265.1	2016-08-17	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by paralogous transcripts.
CCDS44172.1	2016-06-10	This CCDS was updated to remove two 5' prime exons from the transcript because they are not considered to be a part of this gene. The updated protein is shorter at the N-terminus by 15 amino acid residues. 
CCDS5020.3	2016-04-11	The coding region has been updated to shorten the protein N-terminus to one that is more supported by the available transcript and conservation data. The updated protein contains a predicted N-terminal signal peptide, which is consistent with its biological function as a subunit of the GABA receptor complex.
CCDS64463.1	2016-04-07	This CCDS representation lacks full-length INSDC transcript support, but it is supported by full-length SLR-RNA-seq data, including the accessions SRR1803611.78619.1, SRR1803614.53228.1, SRR1660807.243528.1 and ERR279849.4405.1. It is also supported by orthologous transcript alignments and by human RNA-seq data.
CCDS64180.1	2016-03-16	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by partial human transcripts, including DY655290.1 and DY655683.1, and by RNA-seq data.
CCDS6596.2	2016-02-03	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS31541.1	2016-01-28	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS34364.1	2016-01-28	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS33800.1	2016-01-28	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS31710.1	2016-01-28	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS31414.1	2016-01-28	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS31487.1	2016-01-28	This olfactory receptor gene is a segregating pseudogene (PMID:22908908), where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele that is predicted to be non-functional. This CCDS is being retained because the Classifier for Olfactory Receptor Pseudogenes (CORP) predicts the reference genome allele to be functional.
CCDS72854.1	2015-09-24	The coding region has been updated to represent an alternative splice site that is more supported by the available transcript and protein data.
CCDS76390.1	2015-07-27	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by partial human transcript alignments and data in PMID:23122587.
CCDS59225.2	2015-07-27	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by the full-length orthologous mouse transcript U96411.1, by partial human transcript alignments, and by data in PMID:23122587.
CCDS55189.1	2015-07-15	The exon combination of this CCDS representation is inferred based on partial transcript alignments, RNA-seq data and orthologous transcript support from mouse and rat.
CCDS46343.1	2015-07-15	This CCDS representation lacks publicly available full-length transcript support. Its exon combination is based on mRNA annotation on DNA accession AF064205.1 (AAD55812.1 product) from PMID:9799602.
CCDS48167.1	2015-05-19	This CCDS represents the AIFsh2 isoform described in PMID:16644725. The transcript is a candidate for nonsense-mediated mRNA decay (NMD), but the protein is represented based on evidence for the endogenous protein in PMID:16644725.
CCDS34971.1	2015-04-23	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS78241.1	2015-04-14	This gene lacks best hit full-length transcript support, and therefore the exon combination of this CCDS representation is inferred from paralogous transcript alignments.
CCDS76897.1	2015-04-13	This gene lacks full-length transcript support, and thus the exon combination of this CCDS representation is inferred based on paralogous transcript alignments and RNA-seq data.
CCDS76684.1	2015-04-13	This gene lacks full-length transcript support, and therefore the exon combination of this CCDS representation is inferred from partial human transcripts, RNA-seq data and full-length orthologous alignments.
CCDS76588.1	2015-04-13	This gene lacks full-length transcript support, and therefore this CCDS representation is inferred based on partial transcript and RNA-seq alignments.
CCDS76577.1	2015-04-13	This gene lacks full-length transcript support, and therefore this CCDS representation is inferred based on partial transcript alignments, orthologous alignments and RNA-seq data.
CCDS76180.1	2015-04-13	This gene lacks full-length transcript support, and therefore the exon combination of this CCDS representation is inferred based on partial transcript alignments, orthologous alignments and RNA-seq data.
CCDS76106.1	2015-04-13	This PRAME family member lacks best hit transcript support. Thus, the exon combination of this CCDS representation is inferred from paralogous transcript alignments.
CCDS78299.1	2015-04-10	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS78300.1	2015-04-10	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS78301.1	2015-04-10	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS78305.1	2015-04-10	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS77901.1	2015-04-09	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS78298.1	2015-04-09	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS78265.1	2015-04-09	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS76655.1	2015-04-08	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS76450.1	2015-04-08	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by paralogous transcripts. 
CCDS76107.1	2015-04-08	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS76202.1	2015-04-08	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS76201.1	2015-04-08	This CCDS representation lacks full-length human transcript support. Its representation is therefore inferred, but it is supported by paralogous transcripts.
CCDS76206.1	2015-04-06	This CCDS representation has an inferred exon combination due to a lack of full-length transcript support for this gene; it is supported by paralogous gene alignments and data in PMID:16079250.
CCDS46085.1	2014-12-17	This CCDS representation has an inferred exon combination due to a lack of full-length human transcript support for this gene. The represented two-exon structure is supported by orthologous mouse transcript alignments, and by partial human transcript data for the 3' exon.
CCDS58770.1	2014-12-16	The 5'-most in-frame start codon is annotated for this transcript variant, which is supported by mRNA AK126875.1. It is present in a novel exon not found in other transcript variants for this gene. The annotated start codon is restricted to select higher primate species, including human, chimp, gorilla, orangutan and gibbon. It has a weak Kozak sequence and may sometimes be bypassed due to leaky scanning by ribosomes, which could result in use of a better conserved downstream start codon. There is no experimental evidence to indicate which start codon is preferentially used by this variant in vivo.
CCDS47527.2	2014-08-07	The coding region was updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data.
CCDS54617.1	2014-07-30	
CCDS46301.1	2014-07-30	
CCDS45784.1	2014-07-30	
CCDS45283.1	2014-07-30	
CCDS7161.1	2014-07-30	
CCDS3387.1	2014-07-30	
CCDS11882.1	2014-07-25	This CCDS representation is supported by protein evidence in PMIDs 11820818 and 16139264.
CCDS11881.1	2014-07-25	This CCDS representation is supported by protein evidence in PMIDs 11820818 and 16139264.
CCDS45184.1	2014-07-21	The coding region has been updated to correct several errors that were present versus the GRCh38 reference genome assembly.
CCDS41899.1	2014-07-21	The coding region has been updated to remove two codons that are not included in the GRCh38 reference genome allele.
CCDS75845.1	2014-07-18	This CCDS representation is inferred due to a lack of transcript support for this gene. It is supported by paralogous transcript alignments.
CCDS11702.1	2014-06-19	This CCDS representation contains an upstream in-frame start codon that could result in a longer protein N-terminus. However, a downstream start codon is annotated because use of the upstream start codon would eliminate an N-terminal signal peptide, whose presence is consistent with functional support for CD300 family members (e.g., PMIDs 16920917, 19359216).
CCDS55255.1	2014-06-05	The coding region was updated to include a 6-nt insertion found in the GRCh38 reference genome assembly and in aligning transcripts, resulting in two extra amino acids in the protein C-terminus.
CCDS14673.1	2014-05-19	The coding region has been updated to represent the sequence of the GRCh38 reference genome assembly, which results in eight non-synonymous substitutions in the coding region.
CCDS10879.2	2014-05-19	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript and conservation data.
CCDS42364.2	2014-05-19	The coding region has been updated to shorten the N-terminus to one that is more supported by the available protein and conservation data.
CCDS46666.1	2014-04-29	This CCDS representation has been updated to correct a frameshifted segment in the 3' coding region, supported by transcript and orthologous alignments, and by the update of the GRCh37 reference genome assembly to the GRCh38 assembly.
CCDS44052.1	2014-04-21	
CCDS43706.1	2014-03-25	The coding region has been updated to add two internal 6-nt sequences that were included in the update of the GRCh37 reference genome assembly to the GRCh38 assembly. The update results in a protein that is 4 aa longer.
CCDS62957.1	2014-03-25	The coding region has been updated to remove an internal 3-nt sequence that was removed in the update of the GRCh37 reference genome assembly to the GRCh38 assembly. The update results in a protein that is 1 aa shorter.
CCDS8518.1	2013-12-31	
CCDS1796.2	2013-12-04	The coding region has been updated to represent alternative splice sites that are more supported by the available transcript and protein data.
CCDS1785.3	2013-12-03	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript data and by conservation in higher primates.
CCDS47773.1	2013-11-25	
CCDS47233.1	2013-11-25	The exon combination of this CCDS representation is inferred based on available partial human transcript alignments and homology data.
CCDS64784.1	2013-11-25	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 and 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS53985.1	2013-11-25	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 and 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS69299.1	2013-11-25	This exon combination of this CCDS representation lacks support from transcripts deposited in INSDC databases. It represents the Ik-5 variant that is supported by RT-PCR data in PMID:12937159.
CCDS58503.2	2013-11-08	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript data, and by conservation in primates.
CCDS34494.2	2013-10-30	The exon combination of this CCDS representation lacks full-length human transcript support, but it is supported by partial human transcript alignments and by full-length orthologous transcripts, e.g., mouse BC150998.1 or BC151006.1.
CCDS14412.1	2013-10-29	The exon combination of this CCDS representation lacks full-length support from transcripts deposited in INSDC databases, but it is supported by mRNA annotation on DNA accession AY623109.1.
CCDS5873.2	2013-10-21	The coding region has been updated to include an additional codon based on a 3-nt insertion that is present in the GRCh38 reference genome sequence.
CCDS54068.1	2013-10-18	The coding region has been updated to include an additional segment in the coding region. This region corresponds to a tandem repeat encoding a 13 aa segment, which is present 3 times in the reference genome sequence. These tandem repeats are described in PMID:1577776. It should be noted that the majority of available transcript data represent an allele lacking one or more of these repeats, whereas this update represents the number of repeats found in the reference genome sequence.
CCDS61865.1	2013-09-10	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous NPIPA gene alignments.
CCDS61864.1	2013-09-10	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous NPIPA gene alignments.
CCDS61578.1	2013-09-10	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous golgin A8 family alignments.
CCDS61577.1	2013-09-10	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous golgin A8 family alignments.
CCDS64366.1	2013-09-10	This CCDS representation lacks full-length human transcript support and it is therefore inferred. Th full-length exon combination is inferred from partial human transcripts and RNA-seq data.
CCDS61576.1	2013-09-10	The exon combination of this CCDS representation is inferred. It is supported by paralogous golgin A8 family alignments.
CCDS61575.1	2013-11-06	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous golgin A8 family alignments.
CCDS65197.1	2013-09-09	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by partial human transcripts including  AI208887.1, DR007981.1 and DR007982.1. 
CCDS61574.1	2013-09-09	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous golgin A8 family alignments.
CCDS61572.1	2013-09-09	The exon combination of this CCDS representation is inferred. It is supported by partial transcript alignments and by paralogous golgin A8 family alignments.
CCDS61325.1	2013-09-06	The exon combination of this CCDS representation is inferred. It is supported by partial human transcript alignments, RNA-seq data from the Illumina Body Map 2.0 project, and by full-length orthologous transcript alignments, e.g., rat BC097406.1 or mouse BC145796.1.
CCDS60574.1	2013-09-06	The exon combination of this CCDS representation is inferred due to a lack of full-length transcript support for this gene. It is supported by the partial gene-specific EST, HY013942.1, and by full-length transcript alignments from the paralogous NUTM2A gene.
CCDS3700.2	2013-09-05	
CCDS62183.1	2013-09-05	This CCDS represents one of several keratin-associated protein genes located on chromosome 17. This representation is inferred from paralogous and homolgous alignments due to a lack of transcript evidence for this gene.
CCDS42610.1	2013-08-16	This CCDS representation lacks full-length transcript support that is specifically derived from the annotated location. The represented exon combination is inferred from a mixture of partial best hit transcript alignments and paralogous transcript alignments, e.g., from the related LILRA2 locus.
CCDS58639.1	2013-08-06	The expression of the protein represented in this CCDS ID is auto-regulated by polyamine-enhanced translational frameshifting. During translation, a +1 frameshift occurs following codon 68, just preceding a termination codon, thereby enabling translation of the remaining portion of the protein (aa 69-228) in a different reading frame, as experimentally shown for the conserved rat ortholog (PMID:7813017).
CCDS42457.1	2013-08-06	This CCDS ID represents a selenoprotein that is functionally sensitive to selenium levels (e.g., PMID:14642406). Position 73 of the protein is a selenocysteine residue, which is cotranslationally incorporated when a UGA codon, which is normally a stop codon, is recognized by a specific selenocysteyl-tRNA in conjunction with a stem-loop SECIS element in the 3' UTR.
CCDS816.1	2013-08-06	This CCDS representation uses a downstream in-frame AUG start codon, which is supported by homology and publication data. The use of the 5'-most in-frame AUG in the transcript would result in a 74 aa N-terminal extension, but this N-terminal extension is not conserved in other species, and it would eliminate an N-terminal signal peptide, which is known to be present based on experimental evidence (PMIDs 8262907, 3498652).
CCDS55427.1	2013-07-16	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 or 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS53602.1	2013-07-16	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 or 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS53524.1	2013-07-16	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 or 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS53537.1	2013-07-16	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 or 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS54476.1	2013-07-16	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 or 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS54097.1	2013-07-16	This gene represents one of several nuclear copies of the mitochondrial MT-RNR2 gene, which is transcribed as part of the 16S subunit of rRNA and can encode the neuroprotective peptide humanin. RT-PCR evidence in PMID:19477263 suggests that this nuclear gene copy is transcribed. The humanin protein has been detected in vivo (e.g., PMIDs 12009529, 19623253 or 20542501) but it is unclear if this protein is translated from mitochondrial or nuclear gene transcripts. Thus, there is some uncertainty about protein production from this nuclear gene copy. This CCDS is represented because protein production cannot be definitively ruled out for this gene.
CCDS42575.1	2013-06-13	This CCDS ID represents the BCAM transcript variant described in PMIDs 8781446 and 9192786. It encodes the C-terminally truncated 78 kDa isoform described in PMIDs 3810828 and 7777537. The transcript is a candidate for nonsense-mediated mRNA decay (NMD), but the protein is represented because this is the only currently available transcript variant that can encode the 78 kDa isoform. This isoform was detected by immunoblotting in PMID:3810828, and the authors of PMID:7777537 indicate that this isoform was not detected when C-terminal antibodies were used, but it was when antibodies from the region in common with the 85 kDa isoform (CCDS12644.1 representation) were used, thereby suggesting that this C-terminally truncated isoform is valid.
CCDS44873.1	2013-06-06	The full-length exon combination of this CCDS representation is inferred. It is mostly supported by the mRNA AF010403.1, but with correction of a gap in exon 10-11, supported by the mRNA AF010404.1, and by EST, RNA-Seq and orthologous transcript alignments.
CCDS59204.1	2013-05-07	This CCDS represents an inferred full-length model of the OBSCN gene. The exons included in this inferred variant are supported by a combination of available cDNA data and sequence analysis of repetitive exons.
CCDS59435.1	2013-05-07	This CCDS represents an inferred complete model that includes all possible supported in-frame coding exons of the TTN gene. The exons included in this inferred variant are supported by the original sequence analysis and publication data (PMID:11717165), available cDNA and EST data, and additional sequence analysis of the repetitive exons.
CCDS59430.1	2013-04-22	This CCDS representation is supported by 3'-partial AF115505.1. The last four exons are inferred from other aligning transcripts, which do not indicate any alternative splicing in that region. 
CCDS59468.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59459.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59431.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but the full-length exon combination it is supported by partial human transcripts and the full-length paralogous transcript EF523384.1.
CCDS59533.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but the full-length exon combination it is supported by partial human transcripts (AA608988.1 and DB476671.1) paralogous transcript U58096.1.
CCDS59512.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by the full-length paralogous transcript AY037162.1.
CCDS59425.1	2013-09-10	This CCDS representation lacks full-length human transcript support and it is therefore inferred. The full-length exon combination is inferred from the paralogous transcript CA454993.1.
CCDS59497.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by several partial human transcripts including CR748811.1, HY022779.1, HY202236.1 and HY206240.1.
CCDS59360.1	2013-04-08	This gene lacks full-length human transcript support, and therefore the exon combination represented in this CCDS ID is inferred; it is supported by tiled partial transcript alignments (human HY028687.1, DR008137.1, DN831393.1 and others) and by homologous transcript alignments (mouse BC147276.1 and others).
CCDS59471.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59463.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59462.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59461.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59460.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59458.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59457.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59455.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59456.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59454.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59316.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but is supported by other TCEB3 family members including TCEB3C and the mRNA AB076840.1.
CCDS59470.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59469.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59467.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59466.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59464.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59199.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by the full-length paralogous transcript AB084917.1.
CCDS59465.1	2013-04-08	This CCDS representation lacks full-length human transcript support and it is therefore inferred, but it is supported by data in PMID:10936051.
CCDS59507.1	2013-04-05	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by a full-length orthologous mouse transcript, AK302217.1, and partial human transcripts.  
CCDS59221.1	2013-04-05	This CCDS representation lacks full-length human transcript support. Its exon combination is therefore inferred, but it is supported by the full-length orthologous transcript in mouse (AF222444.1). 
CCDS59506.1	2013-04-01	The exon combination of this transcript is based on the paralogous transcript alignment AK026441.1.
CCDS59287.1	2013-03-29	This gene is one of several keratin-associated protein 9 (KRTAP9) genes located on chromosome 17, as described in PMID:11279113. There is no transcript evidence specific for the location of this gene, and therefore this CCDS representation has an inferred structure based on transcript alignments from other family members.
CCDS59286.1	2013-03-29	This gene is one of several keratin-associated protein 9 (KRTAP9) genes located on chromosome 17, as described in PMID:11279113. There is no transcript evidence specific for the location of this gene, and therefore this CCDS representation has an inferred structure based on transcript alignments from other family members.
CCDS59264.1	2013-03-29	This gene is one of several nuclear pore complex interacting protein (NPIP) gene copies that are present on chromosome 16. There are no full-length transcripts derived from this gene copy in support of this CCDS representation, and thus its exon combination is inferred based on paralogous transcript alignments, e.g., the mRNA AF132984.1.
CCDS59263.1	2013-03-29	This gene is one of several nuclear pore complex interacting protein (NPIP) gene copies that are present on chromosome 16. There are no full-length transcripts derived from this gene copy in support of this CCDS representation, and thus its exon combination is inferred based on paralogous transcript alignments, e.g., the mRNA AF132984.1.
CCDS59262.1	2013-03-29	This gene is one of several nuclear pore complex interacting protein (NPIP) gene copies that are present on chromosome 16. There are no full-length transcripts derived from this gene copy in support of this CCDS representation, and thus its exon combination is inferred based on paralogous transcript alignments, e.g., the mRNA AF132984.1.
CCDS59252.1	2013-03-28	This gene represents one of several golgin A8 family genes. This family member lacks full-length transcript support, and thus the exon combination of this CCDS representation is inferred. It is supported by a combination of tiled partial transcript alignments that are specifically derived from this gene, e.g., DB068178.1 and BQ477899.1, and by transcript alignments from other family members.
CCDS59250.1	2013-03-28	The exon combination of this CCDS representation is inferred based on highly similar paralogous transcript alignments, e.g., AY465170.1 or BC101005.1.
CCDS59248.1	2013-03-28	The exon combination of this CCDS representation is inferred based on highly similar paralogous transcript alignments, e.g., AY465170.1 or BC101005.1.
CCDS59509.1	2013-03-25	This CCDS ID represents a 58 aa tumor antigen that is translated from a cryptic ORF at the 3' end of the bicistronic myotrophin transcript. It uses a non-AUG (AUU) translational start codon, as indicated by experimental evidence in PMID:16982933.
CCDS12871.1	2013-03-11	This CCDS representation lacks publicly available transcript support. The represented exon combination is supported by RT-PCR data in PMID:11170751 and by RNA-Seq data from the ENCODE project.
CCDS41905.1	2013-06-19	This CCDS ID represents the protein described in PMIDs: 12364586 and 14966479. This transcript is supported by AY138546.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 18544534. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS53880.1	2013-06-19	This CCDS ID represents the protein described in PMIDs: 12364586 and 14966479. This transcript is supported by AY170469.2. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 18544534. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS13471.1	2013-02-25	This CCDS ID represents the protein described in PMIDs: 20443919 and 19412439. This transcript is supported by AF106697.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in in cow in PMIDs: 9111083 and 10729789. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS47205.1	2013-03-15	This CCDS ID represents the protein described in PMIDs: 10053003, 16737835  and 9889283. This transcript is supported by BC095417.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 10053003 and 16737835.
CCDS44629.1	2013-02-22	This CCDS ID represents the protein described in PMID: 16971948. This transcript is supported by AB209915.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 16971948. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS9181.1	2013-02-21	This CCDS ID represents the protein described in PMID: 9130713 and 9228060. This transcript is supported by BF510077.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously PMID: 18008329.  It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS44494.1	2013-02-21	This CCDS ID represents the protein described in PMID: 17572408. The full-length exon combination of this transcript is based on a combination of mouse (AK220482.1) and human (AK126964.1) partial transcripts. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS1412.1	2013-02-21	This CCDS ID represents the protein described in PMID: 19203586 and is supported by BC014390.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 19203586. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS44029.1	2013-02-15	This CCDS ID represents the protein described in PMIDs: 12724276 and 12207887. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 12724276. Three nearly identical copies of this gene exist on chromosome Y; two copies are part of a palindromic region. This record represents the more centromeric copy within the palindrome.
CCDS44030.1	2013-02-15	This CCDS ID represents the protein described in PMIDs: 12724276 and 12207887. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 12724276. Three identical copies of this gene exist on chromosome Y; two copies are part of a palindromic region. This record represents the more telomeric copy within the palindrome
CCDS14800.1	2013-02-15	This CCDS ID represents the protein described in PMIDs: 12724276 and 12207887. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 12724276. Three identical copies of this gene exist on chromosome Y; two copies are part of a palindromic region. This record represents the copy outside of the palidromic region.
CCDS42981.1	2013-02-13	This CCDS ID represents the protein described in PMIDs: 9923614 and 10215850. This transcript is supported by AF106697.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 9923614. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS34950.1	2013-02-20	This CCDS ID represents the protein described in PMIDs: 10970730 and 17466953. This transcript is supported by BC075802.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously PMID: 17466953. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS3539.1	2013-02-06	This CCDS ID represents the human ortholog of the protein described in PMIDs: 19208547 and 19271754. This transcript is supported by AK057459.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in mouse and rat (PMIDs: 19208547 and 19271754, respectively). It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS2800.1	2013-02-06	This CCDS ID represents the protein described in PMIDs: 10329005 and 9679147. This transcript is supported by AF052224.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMIDs: 9679147 and 19165527. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS871.1	2013-02-05	This CCDS ID represents the protein described in PMIDs: 11437455 and 16111671. This variant is supported by AK056448.1. It should be noted this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 11437455. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS41289.1	2013-02-05	This CCDS ID represents the protein described in PMID: 16792503 and is supported by the mRNA BC069216.1. It should be noted that this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in mouse as shown in PMID: 16792503. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS54.1	2013-02-19	This CCDS ID represents the protein described in PMIDs: 14595118 and 17267690. This protein is encoded by two different splice variants that are supported by AF175409.1 and AL049673.1. It should be noted that this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID: 14595118. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this protein.
CCDS33337.1	2012-11-14	This CCDS ID represents the TTN novex-3 isoform, which has a novel and shorter C-terminus compared to longer isoforms. This isoform is supported by data in PMID:11717165, but it should be noted that the evidence for the transcript is partial on the 5' end, and thus this CCDS representation has an inferred exon combination.
CCDS53542.1	2011-12-01	This CCDS representation is supported by the mRNAs AY674051.1 and AY040091.1. The transcript is a candidate for nonsense-mediated mRNA decay (NMD); however, the protein is represented based on demonstration of the endogenous protein in mouse tissues in PMID:15252030, and because there are no non-NMD transcripts that can encode this protein in either human and mouse.
CCDS9527.3	2011-09-09	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript data. 
CCDS31995.2	2011-09-09	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript data.
CCDS45070.2	2011-09-09	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript data. 
CCDS53593.2	2011-09-07	The coding region has been updated to represent an alternative splicing pattern, resulting in an extended N-terminus that is more supported by the available transcript data and by conservation in primates.
CCDS9815.2	2011-09-07	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript and conservation data.
CCDS9822.2	2011-09-07	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript data and by conservation in higher primates.
CCDS41766.2	2011-09-07	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data.
CCDS9776.2	2011-09-07	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data.
CCDS41858.2	2011-09-07	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data.
CCDS8566.1	2011-06-23	This CCDS represents a TPI variant that uses an internal promoter compared to the CCDS53740.1 representation. Data in PMIDs 4022011, 2925688, 2243103 and 10575546 support the presence of the internal promoter used by this variant. The resulting isoform is 37 aa shorter at the N-terminus compared to the CCDS53740.1 isoform. N-terminal sequencing in PMIDs 9150946 and 9150948 supports the existence of the shorter isoform in vivo.
CCDS53740.1	2011-06-23	This CCDS represents a TPI variant that uses an upstream promoter compared to the CCDS8566.1 representation. Data in PMIDs 4022011, 2925688, 2243103 and 10575546 support the presence of the internal promoter used by the CCDS8566.1 variant. The use of the upstream promoter is supported by human transcript data, including M10036.1, AL517115.3 and DB444195.1, as well as homologous transcripts. This longer transcript also uses an upstream start codon, resulting in an isoform that is 37 aa longer at the N-terminus compared to the CCDS8566.1 isoform. The sequence encoding the longer N-terminus is conserved in most mammalian species.
CCDS44540.1	2011-06-06	This CCDS representation uses a downstream AUG start codon compared to CCDS44539.1. It is supported by the mRNA AK127209.1, which lacks the exon containing the alternative non-AUG (CUG) start codon described in PMID:10321731.
CCDS34305.1	2012-05-24	This CCDS is supported by the mRNA AF155097.1. This mRNA has several mismatches versus the reference genome sequence at this location, and it is unclear if it is derived from this gene (FAM153A) or the similar FAM153B family member (CCDS 43401).
CCDS44423.2	2011-06-02	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data. There are no publicly available full-length transcripts representing this CCDS, but it is supported by the E-26 cDNA described in PMID:1698771.
CCDS44425.2	2011-06-02	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data. There are no publicly available full-length transcripts representing this CCDS, but it is supported by the E-12 cDNA described in PMID:1698771.
CCDS44428.2	2011-06-02	The coding region has been updated to represent an alternative splicing pattern that is more supported by the available transcript and protein data. There are no publicly available full-length transcripts representing this CCDS, but it is supported by the E-3 cDNA described in PMID:1698771.
CCDS4929.2	2011-06-02	The coding region has been updated to extend the N-terminus to one that is more supported by the available transcript data. The updated start codon is found only in primates and it has a weak Kozak signal. It is possible that ribosomal leaky scanning may sometimes allow the better conserved downstream start codon to be used. There is no experimental evidence to indicate which start codon is preferentially used in vivo.
CCDS55301.1	2011-04-22	This CCDS ID represents the most abundant of the shorter human BAG1 isoforms, known as BAG-1S or p36 or p33, as described in the literature, including PMIDs 9396724, 9679980, 9747877 and 17662274. This isoform initiates translation at a downstream AUG start codon. Alternative translation initiation at other AUG start codons produces additional isoforms, known as BAG-1M or p46, and p29. In addition, alternative translation initiation from an upstream non-AUG (CUG) start codon results in the longest human BAG1 isoform, known as BAG-1L or p50. The longest isoform is represented by CCDS 35004.1. Evidence in PMIDs 9747877 and 17662274 indicates that these isoforms have distinct subcellular distributions, which may contribute to the multifunctionality of the protein.
CCDS54453.1	2011-04-20	This CCDS, which is supported by the mRNAs AK289896.1 and BC113854.1, represents a long human HCK isoform, as described in PMIDs 1875927 and 7791757. This isoform initiates translation from a non-AUG (CUG) start codon that is well-conserved and present in a strong Kozak signal context. Alternative translation initiation from a downstream AUG start codon produces an isoform that is 21 aa shorter at the N-terminus. The shorter isoform encoded by this variant is represented by CCDS 54456.1. These isoforms exhibit distinct subcellular distributions, as indicated in PMID:7791757.
CCDS54456.1	2011-04-20	This CCDS, which is supported by the mRNAs AK289896.1 and BC113854.1, represents a short human HCK isoform, as described in PMID:7791757. This isoform initiates translation from a downstream AUG start codon. Alternative translation initiation from an upstream non-AUG (CUG) start codon, which is well-conserved and present in a strong Kozak signal context, produces an isoform that is 21 aa longer at the N-terminus. The longer isoform encoded by this variant is represented by CCDS 54453.1. These isoforms exhibit distinct subcellular localization, as indicated in PMID:7791757.
CCDS54455.1	2011-04-20	This CCDS, which is supported by the mRNAs AK026432.1, BC108930.1 and others, represents a short human HCK isoform, known as p59HCK, as described in PMID:7791757. This isoform initiates translation from a downstream AUG start codon. Alternative translation initiation from an upstream non-AUG (CUG) start codon, which is well-conserved and present in a strong Kozak signal context, produces an isoform that is 21 aa longer at the N-terminus. The longer isoform, which is known as p61HCK, is represented by CCDS 33460.1. These isoforms exhibit distinct subcellular localization, as indicated in PMID:7791757.
CCDS55015.1	2011-04-20	This CCDS, which is supported by the mRNA DQ229900.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 55007.1.
CCDS55013.1	2011-04-20	This CCDS, which is supported by the mRNA AF430806.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 47432.1.
CCDS55014.1	2011-04-20	This CCDS, which is supported by the mRNA BC065522.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 47434.1.
CCDS55011.1	2011-04-20	This CCDS, which is supported by the mRNA AF091352.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 47435.1.
CCDS55012.1	2011-04-20	This CCDS, which is supported by the mRNA BC058855.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 34458.1.
CCDS55008.1	2011-04-20	This CCDS, which is supported by the mRNA AJ010438.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 47433.1.
CCDS55009.1	2011-04-20	This CCDS, which is supported by the mRNA M27281.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 4907.2.
CCDS55010.1	2011-04-20	This CCDS, which is supported by the mRNA S85192.1, represents a VEGFA isoform derived from an AUG start codon. Alternative translation initiation from multiple upstream non-AUG(CUG) codons is also possible for this gene, as indicated in PMIDs:11352659, 11563986 and 11731620. The longest isoform encoded by this variant, which is derived from the 5'-most CUG start codon, is represented by CCDS 34457.1.
CCDS55007.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including DQ229900.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55015.1.
CCDS34458.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. This transcript variant is supported by the full-length mRNA BC058855.1. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55012.1.  
CCDS45881.2	2011-04-20	The coding region has been updated to extend the N-terminus to one that is more supported by available conservation data and publications. There are no publicly available human transcripts that include the extended region. However, the update is supported by homologous transcript data and is consistent with the full-length 190 kDa human isoform described in the literature. This 190 kDa product, known as PHLPP1beta, has been detected in several studies, including PMIDs 17386267, 19079341, 20089132, 20819118 and 20861921.
CCDS32670.1	2011-03-30	This CCDS represents a short variant at the 5' end of a much longer ARHGAP27 gene. The protein includes an SH3 domain.
CCDS3134.1	2014-07-30	
CCDS44334.1	2011-01-11	This CCDS representation uses the 5'-most in-frame translational start codon, as supported by aligning transcript data. It should be noted that this start codon is restricted to higher primate species and is not conserved in other mammals. Lower species use a much better conserved downstream start codon, resulting in a protein that is 142 aa shorter at the N-terminus. It is possible that occasional leaky scanning past the upstream start codon by ribosomes, or alternatively, the presence of a downstream promoter, would sometimes allow use of the downstream start codon in humans. There is no experimental evidence indicating which start codon is preferentially used in vivo.
CCDS44145.1	2010-10-05	This CCDS representation uses a downstream start codon but includes a potential upstream start codon that would result in a protein that is 18 aa longer at the N-terminus. However, the upstream start codon has a weak Kozak signal, the vast majority of transcripts from human and homologous species start downstream of it, and data in PMID:19413330 indicate that the N-terminus begins at an N-alpha acetylated Ala-2 residue (nASIMEGPLSK...) following cleavage of the initiating Met-1 derived from the second start codon. The second start codon is therefore represented in this CCDS.
CCDS41658.1	2010-09-24	This CCDS representation uses a downstream start codon, which is more consistent with the presence of an N-terminal signal peptide, and with experimental evidence for cleavage of this signal peptide in PMID:15340161. It should be noted that an alternative upstream start codon, which would result in a protein that is 38 aa longer at the N-terminus, also exists. However, the use of the upstream start codon would eliminate the signal peptide, and it has a weak Kozak signal, so it is likely that leaky scanning by ribosomes will allow the use of the downstream start codon.
CCDS47815.1	2010-09-23	This variant represents the VMAT1delta15 variant described in PMID:16326835. There are no publicly available transcripts representing it, but it was cloned and characterized in the above publication.
CCDS47282.1	2010-09-21	A downstream start codon is annotated for this CCDS representation because its use is more consistent with the presence of an N-terminal signal peptide in the protein, which is known to contain extracellular cadherin domains. However, it should be noted that an alternative upstream start codon exists, which would result in a protein that is 9 aa longer at the N-terminus and is less likely to contain a signal peptide. The upstream start codon has a weak Kozak signal, so it is possible that leaky scanning by ribosomes will allow the use of the downstream start codon. There is no experimental evidence indicating which start codon is used in vivo.
CCDS47281.1	2010-09-21	A downstream start codon is annotated for this CCDS representation because its use is more consistent with the presence of an N-terminal signal peptide in the protein, which is known to contain extracellular cadherin domains. However, it should be noted that an alternative upstream start codon exists, which would result in a protein that is 9 aa longer at the N-terminus and is less likely to contain a signal peptide. The upstream start codon has a weak Kozak signal, so it is possible that leaky scanning by ribosomes will allow the use of the downstream start codon. There is no experimental evidence indicating which start codon is used in vivo.
CCDS43950.1	2010-08-10	This CCDS representation is supported by the mRNA accession BC069470.1, which has its best hit to this GAGE family member.   
CCDS44150.1	2010-08-03	This CCDS ID represents a variant of the SCP2 locus that uses a downstream promoter, known as the SCP2 promoter. This promoter initiates transcription in an internal exon compared to the longer CCDS572.1 variant, which uses the upstream SCPx promoter. Data in PMIDs 7654720, 7698762 and 14563822, as well as chromatin regulatory features (including Ensembl ENSR00000282553 and ENSR00000282554), support the presence of an active downstream SCP2 promoter.
CCDS44149.1	2010-08-03	This CCDS ID represents a variant of the SCP2 locus that uses a downstream promoter, known as the SCP2 promoter. This promoter initiates transcription in an internal exon compared to the longer CCDS572.1 variant, which uses the upstream SCPx promoter. Data in PMIDs 7654720, 7698762 and 14563822, as well as chromatin regulatory features (including Ensembl ENSR00000282553 and ENSR00000282554), support the presence of an active downstream SCP2 promoter.
CCDS30719.1	2010-08-03	This CCDS ID represents a variant of the SCP2 locus that uses a downstream promoter, known as the SCP2 promoter. This promoter initiates transcription in an internal exon compared to the longer CCDS572.1 variant, which uses the upstream SCPx promoter. Data in PMIDs 7654720, 7698762 and 14563822, as well as chromatin regulatory features (including Ensembl ENSR00000282553 and ENSR00000282554), support the presence of an active downstream SCP2 promoter.
CCDS6037.1	2010-07-29	This CCDS representation uses a downstream AUG start codon. This start codon has a strong Kozak signal and is restricted to human. An upstream start codon, which has a weak Kozak signal and is conserved in some other primates, is also present. The use of the upstream start codon would result in a protein that is 40 aa longer at the N-terminus. However, this would eliminate a signal peptide that is predicted for the shorter but not the longer N-terminus. PMID:9242611 shows experimental evidence for cleavage of a signal peptide following aa 25 from the downstream start, and this is also confirmed in PMID:15340161. Therefore, the downstream start codon is represented for this CCDS.
CCDS47682.1	2010-08-02	This CCDS representation is mostly supported by the long mRNA AB033044.1. However, it should be noted that AB033044.1 contains a chimeric 5' end and lacks the supported start codon for this gene. This CCDS representation therefore uses the expected start codon, with support from other human and homologous transcripts, including human BC030616.2 and several ESTs, mouse BY174440.1 and BY202771.1, and cow EV623524.1, DN286973.1 and AW654672.1.
CCDS46743.1	2010-07-21	This CCDS represents a variant of the ARPC4 locus, and is supported by EST data, including BI768875.1, BQ688329.1, BU161393.1 and BG938423.1. A variant encoding a longer protein is represented by CCDS43047.1.
CCDS46095.1	2010-07-08	The 5'-most start codon based on available transcript data is represented in this CCDS. It should be noted that a possible upstream start codon, which is moderately well-conserved, is present. The use of this upstream start codon would result in a protein that is 15 aa longer at the N-terminus. However, other than AK297891.1, which is a read-through transcript from the upstream ZNF576 locus, there are no human or homologous transcripts supporting extension to this upstream start codon. The 15 aa extension is therefore not included in this CCDS representation.
CCDS47209.1	2010-07-07	This CCDS ID represents the gp130-RAPS isoform described in PMIDs: 10880057 and 16646038. This variant is supported by the transcript AB015706.1. It should be noted that this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID:10880057 using an antibody specific for the distinct C-terminus of this isoform. It is likely that the majority of transcripts representing this variant will undergo NMD, while some low level of NMD escape may allow for the expression of this isoform.
CCDS45605.1	2010-07-07	This CCDS ID represents the p53gamma isoform described in PMIDs: 16131611, 16601753 and 18289041. This variant is supported by the transcript DQ186649.1. It should be noted that this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because other similar isoforms derived from NMD transcripts were detected endogenously in PMID:16131611. In addition, experiments in PMID:17694537 indicate that this gene may be somewhat less sensitive to NMD. A contributing factor is the presence of a ubiquitination domain in the C-terminus of the full-length protein, which makes the protein less stable under non-stress conditions. C-terminally truncated proteins that lack the ubiquitination domain, such as this isoform, are therefore more stable. NMD inhibition experiments in the same study show that the majority of NMD transcripts do indeed undergo NMD, but some low level of NMD escape, combined with the increased stability of C-terminally truncated isoforms, allows for the expression of such isoforms.
CCDS45606.1	2010-07-07	This CCDS ID represents the p53beta isoform described in PMIDs: 16131611, 16601753 and 18289041. This variant is supported by the transcript DQ186648.1. It should be noted that this transcript is predicted to undergo nonsense-mediated mRNA decay (NMD). However, the protein is represented because it was detected endogenously in PMID:16131611 using an antibody specific for the distinct C-terminus of this isoform. In addition, experiments in PMID:17694537 indicate that this gene may be somewhat less sensitive to NMD. A contributing factor is the presence of a ubiquitination domain in the C-terminus of the full-length protein, which makes the protein less stable under non-stress conditions. C-terminally truncated proteins that lack the ubiquitination domain, such as this isoform, are therefore more stable. NMD inhibition experiments in the same study show that the majority of NMD transcripts do indeed undergo NMD, but some low level of NMD escape, combined with the increased stability of C-terminally truncated isoforms, allows for the expression of such isoforms.
CCDS2156.2	2010-07-06	This CCDS representation uses the 5'-most in-frame start codon. While this start codon is well-conserved, it should be noted that other than human and chimp, all other species have indels that follow this start codon. Other primates and rodents have frameshifting indels, and thus cannot use this start codon. However, some mammalian species, including cow, pig and dog, contain additional compensating indels that bring them back in frame; these species could therefore use the start codon represented in this CCDS. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 39 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS42751.1	2010-07-06	This CCDS representation uses the 5'-most in-frame start codon. While this start codon is well-conserved, it should be noted that other than human and chimp, all other species have indels that follow this start codon. Other primates and rodents have frameshifting indels, and thus cannot use this start codon. However, some mammalian species, including cow, pig and dog, contain additional compensating indels that bring them back in frame; these species could therefore use the start codon represented in this CCDS. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 39 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS46525.1	2010-07-06	This CCDS representation is supported by the mRNA AK295564.1. It contains an alternative 5' exon compared to other variants at this locus, as represented by CCDS2460.1 and CCDS46526.1. It should be noted that the annotated start codon in this CCDS has a weak Kozak signal and is only conserved among primate species. It is possible that leaky scanning by ribosomes could occur to allow a downstream start codon to be used at least some of the time. The downstream start codon has a stronger Kozak signal and is much better conserved, and it would result in a protein that is 12 aa shorter at the N-terminus. There is no experimental evidence indicating which start codon is preferentially used by this variant in vivo. Signal peptides can be predicted for both the longer and shorter N-termini (cleavage following aa 31 or aa 19, respectively), but it should be noted that the probability of signal peptide occurrence is reduced for the longer N-terminus, as predicted by SignalP 3.0 and Phobius. It is unknown if a signal peptide is cleaved from the longer protein in vivo.
CCDS44300.1	2010-06-28	This CCDS representation uses the 5'-most in-frame start codon found in the transcript. It should be noted that this start codon has a weak Kozak signal, and its conservation is restricted to primate species, squirrel, rock hyrax and armadillo. Two better conserved potential start codons with stronger Kozak signals are located two and five codons downstream, respectively. It is possible that leaky scanning by ribosomes would allow one of the downstream start codons to be used some of the time. There is no experimental evidence indicating which start codon is preferentially used in vivo.
CCDS1454.1	2010-06-28	This CCDS representation uses the 5'-most in-frame start codon found in the transcript. It should be noted that this start codon has a weak Kozak signal, and its conservation is restricted to primate species, squirrel, rock hyrax and armadillo. Two better conserved potential start codons with stronger Kozak signals are located two and five codons downstream, respectively. It is possible that leaky scanning by ribosomes would allow one of the downstream start codons to be used some of the time. There is no experimental evidence indicating which start codon is preferentially used in vivo.
CCDS1538.1	2010-06-28	This CCDS ID represents the short isoform encoded by this gene. It is also known as 53BP2S, and is described in PMIDs 8668206 and 14766226. This isoform is shorter at the N-terminus compared to the full-length isoform, also known as 53BP2L and represented by CCDS44319.1. The presence of an upstream in-frame start codon, use of which would extend the short isoform N-terminus by 62 aa, should be noted. This has a weak Kozak signal compared to a strong Kozak signal for the represented downstream start codon; the use of the downstream start codon is also supported by in vitro translation experiments in PMID:8668206.
CCDS5855.1	2010-06-25	This CCDS representation uses the 5'-most in-frame start codon. It should be noted that this start codon is restricted to primate species (human, chimp, orangutan, rhesus and marmoset), whereas other mammalian species use a much better-conserved downstream start codon, which has a stronger Kozak signal. It is possible that the first start codon is used in human some of the time, while leaky scanning by ribosomes allows the second start codon to be used more of the time. The use of the latter would reduce the protein length by 1 aa. There is no experimental evidence indicating which start codon is preferably used in vivo.
CCDS5856.1	2010-06-25	This CCDS representation uses the 5'-most in-frame start codon. It should be noted that this start codon is restricted to primate species (human, chimp, orangutan, rhesus and marmoset), whereas other mammalian species use a much better-conserved downstream start codon, which has a stronger Kozak signal. It is possible that the first start codon is used in human some of the time, while leaky scanning by ribosomes allows the second start codon to be used more of the time. The use of the latter would reduce the protein length by 1 aa. There is no experimental evidence indicating which start codon is preferably used in vivo.
CCDS4510.1	2010-06-23	A downstream start codon is used for this CCDS representation based on sequencing of the purified protein in PMID:3063603, which shows that the second in-frame start codon is used. An upstream start codon exists and would result in a protein that is 2 aa longer at the N-terminus, but there is currently no evidence for this longer protein.
CCDS46430.1	2010-06-21	This CCDS representation uses the 5'-most start codon that is available based on current long transcript support for this gene. However, it should be noted that an upstream in-frame start codon is present. The use of this start codon could potentially extend the protein N-terminus by 64 aa. Given the close proximity of this gene to the 5' end of the opposite strand ARL6IP6 gene, most EST evidence that includes this upstream start codon cannot be unambiguously assigned to the PRPF40A gene. In addition, the ESTs DC319474.1, CN365999.1 and DC360797.1 contain an intron that would splice out this start codon, and thus, at least some PRPF40A variants would use the downstream start codon, as represented here.
CCDS45721.1	2010-05-12	Experimental evidence (N-terminal protein sequencing; PubMed ID 10978616) shows a peptide starting at Pro-46, suggesting that the downstream ATG (coding for Met-45) is used.
CCDS5579.1	2010-03-05	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primate species. This starting position is most commonly referred to in the literature, and the numbering system used to describe disease-associated mutations is based on this protein start. This includes data in the P450 oxidoreductase (POR) allele nomenclature locus-specific database, and the Human Gene Mutation Database (HGMD). This start codon is restricted to higher primate species, and it has a weak Kozak signal. However, it should be noted that an alternative downstream start codon, which has a strong Kozak signal and is much more widely conserved, is also present. The use of this downstream start codon would result in a protein that is 3 aa shorter at the N-terminus. Protein sequencing in PMID:2513880 indicates that this is the preferred start codon in vivo. It is therefore possible that the ribosome will initiate at the upstream start codon only a small fraction of the time (if at all), while leaky scanning will allow the downstream start codon to be used predominantly.
CCDS46803.1	2010-03-03	This CCDS representation is supported by the splicing pattern of BC143304.1. It should be noted that this mRNA is 5' partial and does not encode the first 4 aa of the protein. Therefore, this representation includes a 5' extension based on other transcript data at this locus. This extension completes an N-terminal KRAB box, as found in many other zinc finger proteins.
CCDS46802.1	2010-03-03	This CCDS representation is supported by the splicing pattern of BC143332.1. It should be noted that this mRNA is 5' partial and does not encode the first 4 aa of the protein. Therefore, this representation includes a 5' extension based on other transcript data at this locus. This extension completes an N-terminal KRAB box, as found in many other zinc finger proteins.
CCDS34737.1	2010-02-26	This CCDS ID represents the longest MDFIC isoform, known as p40, as described in PMIDs 11139147 and 10671520. This isoform initiates translation at a non-AUG (GUG) start codon that is well-conserved. Alternative translation initiation at a downstream AUG start codon produces an isoform that is 109 aa shorter at the N-terminus, known as p32. These isoforms exhibit distinct subcellular distributions, as indicated in PMID:10671520.
CCDS31539.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. Two alternative downstream start codons also exist, each with stronger Kozak signals and the second being most widely conserved. It is possible that leaky scanning by ribosomes would allow either of the downstream start codons to be used, at least some of the time. The use of a downstream start codon would result in a protein that is 25 aa or 30 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS1633.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in primates, rat, kangaroo rat, dolphin, cow, cat, elephant, tenrec and armadillo. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 2 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS44347.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in primates, rat, kangaroo rat, dolphin, cow, cat, elephant, tenrec and armadillo. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 2 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS44346.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in primates, rat, kangaroo rat, dolphin, cow, cat, elephant, tenrec and armadillo. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 2 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS1632.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in primates, rat, kangaroo rat, dolphin, cow, cat, elephant, tenrec and armadillo. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 2 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS1612.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 1 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS1611.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 1 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS228.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which may be restricted to higher primate species. Two alternative and consecutive downstream start codons, the second of which is most widely conserved, also exist. It is possible that leaky scanning by ribosomes would allow either of the downstream start codons to be used, at least some of the time. The use of a downstream start codon would result in a protein that is 1 aa or 2 aa shorter at the N-terminus. All resulting proteins are predicted to have N-terminal signal peptides, as indicated by SignalP 3.0. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS4188.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 12 aa shorter at the N-terminus. Both the longer and shorter proteins have N-terminal signal peptides, as predicted by SignalP 3.0. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS10880.2	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 4 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS42440.1	2010-03-05	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in other vertebrates, including mouse, opossum, pig and zebrafish. An alternative downstream start codon, which has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 19 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS34034.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 12 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS9606.2	2010-03-05	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in other species. An alternative downstream start codon, which is specific to human and has a slightly stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 2 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS33893.1	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 32 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS7873.2	2010-02-24	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in other species. An alternative downstream start codon, which has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 1 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS33656.1	2010-02-22	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates, cow and dog. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 26 aa shorter at the N-terminus. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS42293.1	2010-02-22	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates. An alternative downstream start codon, which is more widely conserved and has a stronger Kozak signal, also exists. It is possible that leaky scanning by ribosomes would allow the downstream start codon to be used, at least some of the time. The use of the downstream start codon would result in a protein that is 4 aa shorter at the N-terminus. Both the longer and shorter N-termini have predicted signal peptides according to SignalP 3.0. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS5680.1	2010-02-22	This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primates, dog and horse. An alternative downstream start codon also exists, and would result in a protein that is 3 aa shorter at the N-terminus. Both the longer and shorter N-termini have predicted signal peptides according to SignalP 3.0. There is no experimental evidence showing which start codon is preferentially used in vivo.
CCDS35004.1	2011-04-22	This CCDS ID represents the longest human BAG1 isoform, known as BAG-1L or p50, as described in the literature, including PMIDs 9396724, 9679980, 9747877 and 17662274. This isoform initiates translation at a non-AUG (CUG) start codon that is well-conserved and present in a strong Kozak signal context. Alternative translation initiation at downstream AUG start codons produces three additional isoforms with shorter N-termini, known as BAG-1M or p46, BAG-1S or p36 (also known as p33), and p29. The most abundant of the shorter isoforms, BAG-1S, is represented by CCDS 55301.1. Evidence in PMIDs 9747877 and 17662274 indicates that these isoforms have distinct subcellular distributions, which may contribute to the multifunctionality of the protein.
CCDS30558.1	2010-02-12	This CCDS represents the L2betaA isoform of the cyclin L2 locus, as described in PMID:18216018. The transcript is supported by BC016333.1, which is processed at an internal polyA site compared to other transcripts at this locus. The mRNA AK074112.1 also contains the same CDS. However, because the latter mRNA has additional 3' exon structure and the stop codon is present in an internal exon, that transcript is expected to be subject to nonsense-mediated mRNA decay (NMD), whereas transcripts processed at the internal polyA site are predicted to be translated.
CCDS33460.1	2011-04-20	This CCDS, which is supported by the mRNAs AK026432.1, BC108930.1 and others, represents a long human HCK isoform, known as p61HCK, as described in PMIDs 1875927 and 7791757. This isoform initiates translation from a non-AUG (CUG) start codon that is well-conserved and present in a strong Kozak signal context. Alternative translation initiation from a downstream AUG start codon produces an isoform that is 21 aa shorter at the N-terminus. The shorter isoform, which is known as p59HCK, is represented by CCDS 54455.1. These isoforms exhibit distinct subcellular distributions, as indicated in PMID:7791757.
CCDS47434.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including BC065522.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55014.1.
CCDS34457.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including S85192.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55010.1.
CCDS47432.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including AF430806.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55013.1.
CCDS47433.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including AJ010438.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55008.1.
CCDS47435.1	2011-04-20	This CCDS representation starts at an upstream non-AUG (CUG) translation start codon that is supported by conservation data and experimental evidence, including that in PMIDs:11352659, 11563986 and 11731620. Most of the publicly available long mRNAs at this locus do not extend far enough 5' to include the CUG start codon, including AF091352.1 which supports this variant. However, BC058855.1, several unspliced partial transcripts and the aforementioned publications all support transcription initiation further upstream. Hence, this CCDS representation includes the extended 5' CDS. Alternative translation initiation from a downstream AUG codon (Met-181), which results in a shorter isoform with a predicted signal peptide, has also been shown for this gene. The shorter isoform encoded by this variant is represented by CCDS 55011.1.
CCDS32519.2	2009-11-20	The coding region has been updated to remove a 30-nt insert that is absent in the GRCh37 reference genome assembly. The CDS of this locus includes a tandem repeat sequence that is present 17 times in the reference genome assembly; the removed 30-nt insert corresponds to an additional repeat. Transcript data indicate that alleles contain variable copy numbers of this tandem repeat.
CCDS34108.1	2009-11-06	This CCDS representation is supported by transcript data, including the mRNAs BC088357.1 and AK313221.1. The 5'-most in-frame translational start codon is annotated, but it should be noted that this start codon is specific to primate species. This start codon also has a weak Kozak signal, and thus it is possible that leaky scanning by the ribosome will sometimes occur to allow initiation at a downstream start codon. The downstream start codon has a stronger Kozak signal and is much more widely conserved. Translation from the downstream start codon would result in a protein that is 11 aa shorter at the N-terminus. An alternative 5' end variant that encodes the shorter protein is represented by CCDS3831.1. 
CCDS1669.1	2009-09-28	This CCDS represents the transcript derived from the downstream promoter of this gene. Studies in both PMIDs 10631117 and 11978970 support the presence of the downstream promoter, as do the 5' extents of several human and homologous transcripts. PMID:11978970 also provides evidence for an upstream promoter; the transcript derived from the upstream promoter would encode a protein that is 60 aa longer at the N-terminus.
CCDS43013.1	2009-09-28	This CCDS representation is supported by accession DQ778625.1. It includes an alternative splice acceptor for exon 10 compared to the variants represented by NM_014309.2 (CCDS13921.1) and NM_001082576.1 (CCDS46701.1). This is a non-canonical 'GG' splice acceptor site as compared to the 'AG' acceptor found in NM_014309.2 and NM_001082576.1, but the 'GG' splice acceptor is supported by 30 human transcripts and by transcripts in other species, including mouse (e.g., AK139555.1, AK077594.1, AK055213.1, AY659953.1, DQ017388.1 and several ESTs), rat (BC128766.1, BM388666.1), cow (BT026301.1 and several ESTs), pig (AK236515.1 and a few ESTs), sheep (EE755507.1, EE862219.1) and dog (CO666028.1, CO586266.1).
CCDS42703.2	2009-08-24	The coding region has been updated to remove a 3-nt insert (encoding Ser-310) that was present in the NCBI Build 36 reference genome assembly. This insert has been removed in the GRCh37 reference genome, and its absence is supported by transcript data.
CCDS35438.1	2009-07-29	The translation initiation codon selected for this CCDS representation has a strong Kozak signal, but it appears to be human-specific. A much better-conserved alternate start codon, which also has a strong Kozak signal, exists further downstream. Use of the downstream start codon would result in a protein that is 10 aa shorter at the N-terminus. No experimental evidence exists to indicate which start codon is used in vivo.
CCDS3225.1	2009-07-27	This CCDS representation is supported by accession AF204159.1 and data in PMID:10766764.
CCDS33268.1	2009-07-16	This CCDS representation does not have any full-length human transcript support, but it is supported by overlapping partial transcript evidence, including AF432211.1, AK090813.1, AK308707.1, and several tiled ESTs. This representation is also supported by studies in PMID:18946081, which functionally characterizes this protein, and by homology support in mouse (NP_081651.2, CCDS23859.1) and rat (NP_001101103.1). PMID:18243103 also describes a partial crystal structure for this protein.
CCDS33650.1	2009-07-03	This CCDS representation is based on X83705.1. Although this mRNA accession lacks the final two exons, data in PMID:7659502 support the full-length nature of the transcript, and also the presence of a functional promoter at the 5' end.
CCDS33255.1	2009-07-02	This CCDS representation is based on AB083211.1 and is supported by data in PMID:14985102. This publication also shows the existence of this variant in mouse, as well as the presence of this truncated isoform in various mouse tissues in vivo.
CCDS2342.1	2009-07-02	This CCDS representation is based on AF422928.1 and U58143.1, and on data in PMID:11917123. This 479 aa isoform is also supported by homologous proteins, including pig NP_001026949.1, cow NP_001039435.1, mouse NP_033942.1, rat NP_071613.1 and chicken NP_989923.1. In addition, macaque AB172864.1 supports the full-length splice pattern. 
CCDS42803.1	2009-07-02	This CCDS representation is based on U90273.1 and on full-length RT-PCR evidence from PMIDs 10831323 and 10556814. This variant also has homology support from cow AF539438.1, mouse U90270.1 and rat U90271.1.
CCDS43935.1	2009-07-02	SSXB4 is identical to SSX4 as it produces the same protein product. This protein is likey to be functional despite arising from a duplication, therefore this CCDS has been retained.
CCDS35085.1	2009-06-23	This CCDS ID is based on a transcript that is a candidate for nonsense-mediated decay (NMD); however, the protein is supported by experimental evidence (PMID 7737358, 12747772) and by protein homology.
CCDS716.1	2009-06-22	This CCDS represents a retrogene of RBMX (RNA binding motif protein, X-linked), which is located on chromosome X. While all introns in the coding sequence have been processed out compared to the RBMX locus, the ORF is intact and there is specific evidence for transcription at this location. Studies in PMID:16201836 indicate that this locus is likely to be functional because the ORF has been preserved by purifying selection in all six Old World primates carrying this retrogene. Given that X chromosomal genes in mammals can generate a statistically significant excess of autosomal retrogenes relative to genes on other chromosomes (PMID:14739461), it is possible that this retrogene may be functional during male meiosis when X chromosomal genes are silenced or during haploid stages of spermatogenesis (PMID:16201836). In addition, it should be noted that this retrogene shares its first non-coding exon with the cysteine conjugate-beta lyase 2 (CCBL2) locus on chromosome 1, but the coding sequences are non-overlapping.
CCDS8646.1	2009-06-18	This CCDS ID is based on AF281255.1. This transcript appears to be a nonsense-mediated mRNA decay (NMD) candidate; however, there are publications describing this transcript and its encoded protein (Guo et al, 2001, PMID 11054413; Liu et al, 2008, PMID 18006276) so this CCDS ID has been retained. 
CCDS9573.1	2009-02-19	This CCDS ID represents the most N-terminally extended OXA1L protein, which is derived from the 5'-most translation start codon of the transcript (nt 1 of NM_005015.3). This AUG codon has a weak Kozak signal, compared to a strong Kozak signal for a downstream in-frame AUG (nt 40 of NM_005015.3). Translation from this second AUG would result in a protein that is 13 aa shorter at the N-terminus. Due to leaky scanning by ribosomes, it is possible that some ribosomes may initiate translation at the first AUG codon, while others may initiate at the second AUG. A third in-frame AUG codon is also present further downstream (nt 181 of NM_005015.3), translation from which would result in a protein that is 60 aa shorter at the N-terminus. Experimental evidence in PMID:12972568 suggests that the 60 aa shorter protein can function better than the longest protein to complement the respiratory growth defect of yeast oxa1 cells. However, the longest protein still retained some function. There is no experimental evidence examining the function of either protein in human cells, or no indication of which start codon is preferentially used in human cells.
CCDS7620.2	2009-01-30	A downstream AUG translation start codon is selected for this CCDS representation based on a strong community standard for its use, and on a higher probability of a signal peptide being present in the protein N-terminus. The use of an alternative upstream AUG start codon would result in a protein that is 19 aa longer at the N-terminus. The upstream AUG has a weak Kozak signal while the downstream AUG has a strong Kozak signal. Due to leaky scanning by ribosomes, it is possible that some ribosomes may initiate translation from the downstream AUG codon while others start from the upstream AUG. The presence of multiple upstream ORFs suggests that a combination of leaky scanning and translational reinitiation may be necessary to achieve translation of the annotated ORF.
CCDS31298.1	2009-01-26	A downstream AUG translation start codon is selected for this CCDS representation based on a strong community standard for its use, and on a higher probability of a signal peptide being present in the protein N-terminus. The use of an alternative upstream AUG start codon would result in a protein that is 19 aa longer at the N-terminus. The upstream AUG has a weak Kozak signal while the downstream AUG has a strong Kozak signal. Due to leaky scanning by ribosomes, it is possible that some ribosomes may initiate translation from the downstream AUG codon while others start from the upstream AUG. The presence of multiple upstream ORFs suggests that a combination of leaky scanning and translational reinitiation may be necessary to achieve translation of the annotated ORF.
CCDS10234.1	2009-01-19	This CCDS ID represents a variant of the RPLP1 gene that is based on a splice pattern found in several ESTs, including BM768334.1, BM508180.1, EL948616.1 and AJ713466.1.
CCDS5607.1	2009-01-19	This CCDS ID represents variant C of the ABCB4 gene, which is based on experimental evidence described in PMID:2892668.
CCDS5566.2	2009-01-09	The coding region has been updated to represent an alternate splice pattern, resulting in an alternate and longer C-terminus that is better supported by available transcript and conservation data.
CCDS11926.2	2009-01-05	The coding region has been updated to include additional exons at both the 5' and 3' ends, resulting in an extension of both the N- and C-termini. There are no full-length human transcripts representing this gene, but the update is supported by available overlapping partial transcripts, by conservation data, and by data included in PMID:17549423.
CCDS10238.2	2009-01-05	The coding region has been updated to include additional 5' exons and to extend the N-terminus to one that is more supported by available transcript and conservation data. The update adds an additional TSP1 (Thrombospondin type 1 repeats) domain and an Adam_spacer 1 domain to the protein.
CCDS6396.1	2008-10-06	This CCDS represents the shorter LY6H isoform. NM_002347.4 is based on an alternative 5' end, as found in the ESTs DB471677.1, BP347868.1 and EB385547.1. Other alternative 5' ends exist, as in AK314139.1, BC028894.1, AB012293.1 and BC030192.1, and these contain an upstream in-frame translation start codon which results in an isoform that is 21 aa longer at the N-terminus. The upstream start codon has a weaker Kozak signal than the downstream start codon, so these variants may also produce the shorter isoform, as suggested in PMID:9799603.
CCDS6370.1	2008-09-11	This CCDS represents a 276 aa protein that is encoded by NM_001045556.2, which is based on BX648382.1 and several locally supporting ESTs. However, it should be noted that NM_001045556.2 contains an upstream translation start codon at nts 504-506, as used in the NM_001045557.2 variant which encodes a 293 aa protein. The use of this upstream start codon in NM_001045556.2 would result in only a 15 aa ORF with a stop codon in the second exon. The short length of this upstream ORF may allow escape from nonsense-mediated mRNA decay (NMD) and translation reinitiation at the downstream start codon (nts 833-835) to encode the represented 276 aa protein, or alternatively, the weak Kozak signal at the upstream start codon may enable leaky scanning by the translation machinery and subsequent use of the downstream start codon. The 276 aa protein is consistent with reports in the literature, including PMIDs:7543898, 8825655 and 9660183. Variants encoding both the longer and shorter isoforms are also present in mouse (NM_001029841.3 and NM_009192.2, respectively).
CCDS7709.1	2008-08-28	No human mRNA or EST accessions have been deposited in public databases to support this CCDS, but the gene, transcript and protein have been well-characterized in the literature, e.g., PMIDs:2315322, 12160732, 15706223 and 16888198. Secretin proteins in other species also support this CCDS.
CCDS7564.2	2008-07-22	The coding region has been updated to include an alternative exon that is more supported by the available transcript and protein data. The update completes the helix-loop-helix dimerization domain, which was previously truncated.
CCDS13677.1	2008-07-03	This CCDS ID represents a splice variant of the C2CD2 gene, compared to the longer variant which is represented by CCDS42933.1. The splice pattern of this shorter variant is supported by AL833323.1. This variant contains an alternative 5' end, which is also supported by BM051485.1, and it lacks the first two coding exons found in the longer variant, resulting in the use of an in-frame downstream translation start codon compared to the longer variant. This shorter variant is considered to be protein-coding in the absence of evidence suggesting otherwise.  
CCDS4579.1	2008-07-03	This CCDS ID represents a variant of the HFE gene that lacks an internal coding exon compared to the longest variant, which is represented by CCDS4578.1. This results in an isoform that includes the Immunoglobulin constant region (IGc) domain but lacks a portion of the Class I Histocompatibility antigen (MHC_I) domain.
CCDS4578.1	2008-07-03	This CCDS ID represents the longest isoform encoded by the HFE gene. This isoform contains both a Class I Histocompatibility antigen (MHC_I) and an Immunoglobulin constant region (IGc) domain.
CCDS4582.1	2008-07-03	This CCDS ID represents a variant of the HFE gene that lacks three internal coding exons compared to the longest variant, which is represented by CCDS4578.1. This results in an isoform that lacks both the Class I Histocompatibility antigen (MHC_I) and Immunoglobulin constant region (IGc) domains.
CCDS4581.1	2008-07-03	This CCDS ID represents a variant of the HFE gene that lacks two internal coding exons compared to the longest variant, which is represented by CCDS4578.1. This results in an isoform that lacks the entire Class I Histocompatibility antigen (MHC_I) domain, but the Immunoglobulin constant region (IGc) domain is included.
CCDS4580.1	2008-07-03	This CCDS ID represents a variant of the HFE gene that lacks an internal coding exon compared to the longest variant, which is represented by CCDS4578.1. This results in an isoform that includes the Immunoglobulin constant region (IGc) domain but lacks a portion of the Class I Histocompatibility antigen (MHC_I) domain.
CCDS41947.1	2008-07-03	This CCDS ID represents the longer isoform encoded by the TRAPPC6B gene. The shorter isoform is represented by CCDS9670.1.
CCDS9670.1	2008-07-03	This CCDS ID represents the shorter isoform encoded by the TRAPPC6B gene. Although this protein lacks a segment of the predicted TRAPP_Bet3 domain compared to the longer isoform (represented by CCDS41947.1), there are several transcripts supporting this shorter variant, and there is no experimental evidence indicating that this variant does not encode a protein.
CCDS11839.2	2008-07-03	The coding region has been updated to represent an alternative 3' splice pattern, resulting in a longer and distinct C-terminus that is better supported by available transcript and homology data. In addition to the three MBT repeats and the C2HC type zinc finger domain included in this protein, the update adds a SAM_1 (Sterile alpha motif) domain, which is a widespread domain in signaling and nuclear proteins.
CCDS7726.2	2008-07-03	The coding region has been updated to represent an alternative 3' splice pattern, resulting in a longer and distinct C-terminus that is better supported by available transcript and homology data. The update adds two C2 domains (Ca2+-dependent membrane-targeting modules), which are hallmarks of synaptotagmin proteins.
CCDS10689.2	2008-07-03	The coding region has been updated to add an additional internal exon and to extend the N-terminus to one that is more supported by available transcript and conservation data. The N-terminal extension adds a HSA domain (found in DNA binding proteins and often associated with helicases) to the DEXDc, HELICc and AT_hook domains that are also found in this protein, and this is consistent with the function of this protein as a DNA helicase.
CCDS3411.2	2008-08-26	The coding region has been updated to extend the C-terminus following the addition of several exons at the 3' end. There are no full-length transcripts representing the update, but partial transcripts do span its length in both human and the mouse ortholog. The updated sequence includes a large exon 10 that has no single transcript spanning its full extent. Nonetheless, BX648206.1 covers most of this exon, as does AB037748.2, which is spliced to the 3' neighboring exons. AF528529.1 and AK090534.1 are spliced to the 5' neighboring exons, supported by orangutan CR860680.1. Several tiled transcripts also span this exon in mouse, including AK140021.1, AF013969.1 and AK122495.1. Some transcripts appear to have polyA tails and terminate in this large exon, e.g., BX648206.1, AK025965.1 and AF528529.1, but on closer inspection, it appears that these may be priming off internal 'A' nucleotides in exon 10, and they do not have polyA signals. The open reading frame represented in the update also shows good conservation in models from other species, including macaque XP_001098928.1, dog XP_536235.2, cow XP_585315.3, chicken XP_420784.2, and rat XP_001060944.1. It is also of note that the genomic alignments between these species show insertions/deletions in the region of exon 10 that are always in multiples of three, or else they are compensated in order to restore the reading frame. This is a strong signature of a protein-coding region and provides good supporting evidence for the validity of this exon/intron structure.
CCDS229.2	2008-07-01	The coding region has been updated to represent an alternative 3' splice pattern, resulting in a shorter and distinct C-terminus that is better supported by available transcript and homology data.
CCDS10120.2	2008-07-01	The coding region has been updated to extend both the N- and C-termini based on available transcript data. The update is based on the splice pattern of AK096267.1, a full-length mRNA. The same protein is described in PMID:11095946, but the published sequence is over-extended by 57 aa at the N-terminus due to the presence of an uncorrected 5' mismatch compared to the reference genome sequence.
CCDS10856.1	2008-06-27	The translation start codon selected for this CCDS is conserved in primates. A possible downstream translation start codon, which is better conserved across species and is consistent with the dipeptidase 2 family member, would reduce the protein length by 25 aa. No experimental evidence exists regarding which start codon is used.
CCDS33159.2	2008-06-27	There is only one full-length mRNA, AY358172.1, that supports this CCDS splice variant although it is different at the 3' end. The 3' end of AY358172.1  would cause it to be an NMD candidate. The 3' end is supported by BC043211.1, AK122995.1 and AY358214.1 although these have extra internal exons that are not in the RefSeq. Mouse ESTs, BB730166.1 and BB728829.1, support the 3' end. Human ESTs, BI559800.1, DC308501.1, and BX118758.1, show support for some splice sites but also include additional exons. The protein encoded by this CCDS contains intact PFAM Latrophilin/CL-1-like GPS (GPS) and the 7 transmembrane receptor (Secretin family) (7tm_2) domains. Given the current evidence at this locus, this is the best variant that can be represented; this could change with future transcript evidence. It seems that a combination of AY358172.1 5' and 3' ends and the inclusion of the extra AY140955.1 exons in the middle could also create a valid splice variant but there is not enough evidence for this at this time.
