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Anole lizard assembly and gene annotation

The Carolina anole (Anolis carolinensis) is an arboreal anole lizard native to the southeastern United States (west to Texas) and introduced elsewhere. This species has been chosen as a model reptile for genomics by the NHGRI because of the ease and low cost of laboratory breeding and evolutionary value of the diversity of the genus.


AnoCar2.0 (GCA_000090745.1) is an assembly of the anole lizard, provided by the Genome Sequencing Platform, the Genome Assembly Team, Broad Institute of MIT and Harvard. This assembly is used by UCSC to create their anoCar2 database.

The anole lizard genome is composed of 13 chromosomes, assembled from 41.9861 contigs and 2.143 scaffolds. The total number of bases in the genome is 1.78Gb.

Gene annotation

The gene set for anole lizard was built using the Ensembl genebuild pipeline. Gene models are based on genewise alignments of chicken proteins as well as genetically distant proteins from other species, including most vertebrates from Uniprot. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. The protein based gene models were then extended using anole lizard cDNA and EST alignments as well as chicken cDNA. Potentially missing predictions and partial gene predictions were identified by examining the human-chicken one-to-one orthologs, which were then used to build new gene models.

RNASeq data set

In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt vertebrate proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

TissueNumber of gene models
adrenal gland22213
skeletal muscle22316
whole embryo22958

More information

General information about this species can be found in Wikipedia.



AssemblyAnoCar2.0, INSDC Assembly GCA_000090745.1, May 2010
Base Pairs1,701,353,770
Golden Path Length1,799,143,587
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2010
Genebuild releasedDec 2010
Genebuild last updated/patchedJul 2016
Database version100.2

Gene counts

Coding genes18,595
Non coding genes7,168
Small non coding genes2,883
Long non coding genes4,008
Misc non coding genes277
Gene transcripts27,172


Genscan gene predictions107,132

About this species