Human assembly and gene annotation

Assembly

This site provides a data set based on the February 2009 Homo sapiens high coverage assembly GRCh37 from the Genome Reference Consortium. This assembly was used by UCSC to create their hg19 database. The data set consists of gene models built from the genewise alignments of the human proteome as well as from alignments of human cDNAs using the cDNA2genome model of exonerate.

This release of the assembly has the following properties:

  • 27478 contigs.
  • contig length total 3.2 Gb.
  • chromosome length total 3.1 Gb.

It also includes nine haplotypic regions, mainly in the MHC region of chromosome 6.

Patches

As the GRC maintains and improves the assembly, patches are being introduced. Currently, assembly patches are of two types:

  • Novel patch: new sequences that add alternative sequence at a loci and will remain as haplotypes in the next major assembly release by GRC
  • Fix patch: sequences that correct the reference sequence and will replace the given region of the reference assembly at the next major assembly release by GRC

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001405.14

Other assemblies

Gene annotation

The Ensembl human gene annotations have been updated using Ensembl's automatic annotation pipeline. The updated annotation incorporates new protein and cDNA sequences which have become publicly available since the last GRCh37 genebuild (March 2009).

This archive displays a joint gene set based on the merge between the automatic annotation from Ensembl and a freeze of the manual annotation from Havana (first published in Vega Release 55). Transcripts from the two annotation sources are merged if they share the same internal exon-intron boundaries (i.e. have identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Havana transcripts are included in the final Ensembl/Havana merged (GENCODE) gene set. See the summary table opposite for the corresponding GENCODE version number. The Consensus Coding Sequence (CCDS) identifiers have also been mapped to the annotations. More information about the CCDS project.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyGRCh37.p13 (Genome Reference Consortium Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009
Database version88.37
Base Pairs3,326,743,047
Golden Path Length3,098,825,702
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJul 2010
Genebuild releasedApr 2011
Genebuild last updated/patchedSep 2013
Gencode versionGENCODE 19

Gene counts (Primary assembly)

Coding genes20,805 (incl 463 readthrough)
Pseudogenes14,181 (incl 4 readthrough)
Gene transcripts196,501

Gene counts (Alternative sequence)

Coding genes2,606 (incl 37 readthrough)
Pseudogenes1,730

Other

Genscan gene predictions48,597
Short Variants156,229,297
Structural variants5,742,050

About this species