(Graphic courtesy of CBSE)
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Homo sapiens (Graphic courtesy of CBSE) |
The February 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium. For more information about this assembly, see GRCh37 in the NCBI Assembly database.
A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST or STS marker, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the human genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
|
| chr7 | Displays all of chromosome 7 | |
| chrUn_gl000212 | Displays all of the unplaced contig gl000212 | |
| 20p13 | Displays region for band p13 on chr 20 | |
| chr3:1-1000000 | Displays first million bases of chr 3, counting from p-arm telomere | |
| chr3:1000000+2000 | Displays a region of chr3 that spans 2000 bases, starting with position 1000000 | |
|
RH18061;RH80175 15q11;15q13 rs1042522;rs1800370 |
Displays region between genome landmarks, such as the STS markers RH18061 and RH80175, or chromosome bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax may also be used for other range queries, such as between uniquely determined ESTs, mRNAs, refSeqs, etc. | |
| D16S3046 | Displays region around STS marker D16S3046 from the Genethon/Marshfield maps. Includes 100,000 bases on each side as well. | |
| AA205474 | Displays region of EST with GenBank accession AA205474 in BRCA1 cancer gene on chr 17 | |
| AC008101 | Displays region of clone with GenBank accession AC008101 | |
| AF083811 | Displays region of mRNA with GenBank accession number AF083811 | |
| PRNP | Displays region of genome with HUGO Gene Nomenclature Committee identifier PRNP | |
| NM_017414 | Displays the region of genome with RefSeq identifier NM_017414 | |
| NP_059110 | Displays the region of genome with protein accession number NP_059110 | |
| pseudogene mRNA | Lists transcribed pseudogenes, but not cDNAs | |
| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| huntington | Lists candidate genes associated with Huntington's disease | |
| zahler | Lists mRNAs deposited by scientist named Zahler | |
| Evans,J.E. | Lists mRNAs deposited by co-author J.E. Evans | |
| Use this last format for author queries. Although GenBank requires the search format Evans JE, internally it uses the format Evans,J.E.. | ||
The GRCh37 build reference sequence is considered to be "finished", a technical term indicating that the sequence is highly accurate (with fewer than one error per 10,000 bases) and highly contiguous (with the only remaining gaps corresponding to regions whose sequence cannot be reliably resolved with current technology). Future work on the reference sequence will focus on improving accuracy and reducing gaps in the sequence. Statistics for the GRCh37 build assembly can be found on the NCBI Build 37.1 Statistics web page. For a glossary of assembly-related terms, please see the GRC Assembly Terminology page.
Note on chrM
Since the release of the UCSC hg19 assembly, the Homo sapiens
mitochondrion sequence used as "chrM" in the Genome Browser,
NC_001807,
has been replaced in GenBank with the record
NC_012920,
the Revised Cambridge
Reference Sequence (rCRS).
We have not replaced the chrM sequence in the hg19 Genome Browser.
However, in March 2020 we added the rCRS sequence to hg19 separately as "chrMT".
In the latest human assembly release (Dec. 2013, GRCh38/hg38), "chrM" is the rCRS
and NC_001807 is not included.
Chromosome naming scheme
In addition to the "regular" chromosomes, the hg19 browser contains
9 alternative haplotype sequences, 39 unplaced contigs, and 20 unlocalized contigs
from the initial GRCh37 assembly release.
In March 2020 we added patch sequences from GRC patch release 13 (GRCh37.p13):
73 "novel" patches (alternative haplotype sequences) and 131 "fix" patches
(corrected sequences).
For unlocalized contigs, the contig name is appended to the regular chromosome
name, as in chr1_gl000191_random. If the chromosome is unknown, the
contig is represented with the name "chrUn" followed by the contig
identifier, as in chrUn_gl000211. Note that the chrUn contigs are no
longer placed in a single, artificial chromosome as they have been in previous UCSC
assemblies.
The 9 alternative haplotypes released with the original assembly are shown in the
table below. For subsequent alternative haplotype patches the regular chromosome
name is followed by the contig accession and then "_alt", for example
chr5_gl339449_alt. Fix sequences introduced by patches are named in a similar
fashion but with "_fix" instead of "_alt", e.g. chrX_jh806590_fix.
Additional information on alt and fix sequences can be found in our
FAQ. See the
sequences page for a complete list of
hg19 sequences.
The nine haplotype sequences in the initial GRCh37 release are named:
| name | accession | UCSC chr name |
|---|---|---|
| HSCHR6_MHC_APD_CTG1 | GL000250.1 | chr6_apd_hap1 |
| HSCHR6_MHC_COX_CTG1 | GL000251.1 | chr6_cox_hap2 |
| HSCHR6_MHC_DBB_CTG1 | GL000252.1 | chr6_dbb_hap3 |
| HSCHR6_MHC_MANN_CTG1 | GL000253.1 | chr6_mann_hap4 |
| HSCHR6_MHC_MCF_CTG1 | GL000254.1 | chr6_mcf_hap5 |
| HSCHR6_MHC_QBL_CTG1 | GL000255.1 | chr6_qbl_hap6 |
| HSCHR6_MHC_SSTO_CTG1 | GL000256.1 | chr6_ssto_hap7 |
| HSCHR4_1_CTG9 | GL000257.1 | chr4_ctg9_hap1 |
| HSCHR17_1_CTG5 | GL000258.1 | chr17_ctg5_hap1 |
See the Wellcome Trust Sanger Institute MHC Haplotype Project web site for additional information on the chr6 alternate haplotype assemblies.
The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates:
chrY:10001-2649520 and chrY:59034050-59363566
chrX:60001-2699520 and chrX:154931044-155260560
For further information on GRCh37 build see the NCBI GRCh37 release notes.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. We recommend that you use rsync for downloading large or multiple files.
The hg19 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.