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Macaque assembly and gene annotation

Assembly

The Mmul_10 assembly was submitted by The Genome Institute at Washington University School of Medicine on March 2019. The assembly is on chromosome level, consisting of 3,182 contigs assembled into 2,979 scaffolds. From these sequences, 22 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 46,608,966 while the scaffold N50 is 82,346,004.

Gene annotation

The annotation for the protein -coding genes was carried out using three main techniques:

  • Rhesus macaque RNA-seq data from thirteen tissues.
  • Whole genome alignment against the human GRCh38 assembly followed by projection of GENCODE Basic protein-coding transcripts in regions of sufficient alignment conservation.
  • Splice-aware alignment of a subset of UniProt proteins to the Mmul_8.0.1 assembly.

The subset of UniProt proteins used was our 'primates basic' set. This consisted of the proteins from the following clades and protein existence (PE) levels:

  • Human PE level 1 & 2 proteins.
  • Other primates PE level 1, 2 & 3 proteins.
  • Mouse PE level 1 & 2 proteins.
  • Other mammals PE level 1 & 2 proteins.
  • Other vertebrates PE level 1 & 2 proteins.

UTRs were obtained (where possible) from the RNA-seq data and alignments of RefSeq rhesus macaque cDNAs.

Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.

Long intergenic ncRNAs were annotated from transcripts produced during the RNA-seq pipeline that had either a poor or no BLAST hit to any UniProt vertebrate PE12 protein. These transcripts are then scanned for evidence of protein domains. If no evidence was found the model was marked as lincRNA.

The annotation process is described in the document below.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyMmul_10, INSDC Assembly GCA_003339765.3, Feb 2019
Base Pairs2,971,331,530
Golden Path Length2,971,331,530
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedDec 2019
Database version100.10

Gene counts

Coding genes21,761
Non coding genes12,904
Small non coding genes4,712
Long non coding genes4,773
Misc non coding genes3,419
Pseudogenes767
Gene transcripts64,228

Other

Genscan gene predictions47,724
Short Variants51,642,961
Structural variants110

About this species

HASH(0x22c89a80)