Anole lizard assembly and gene annotation

Assembly

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.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000090745.1

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
brain23145
dewlap25201
heart23246
liver23169
lung22811
merged27722
ovary25003
skeletal muscle22316
whole embryo22958

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAnoCar2.0, INSDC Assembly GCA_000090745.1, May 2010
Database version78.2
Base Pairs1,701,353,770
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

1,799,143,587
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2010
Genebuild releasedDec 2010
Genebuild last updated/patchedFeb 2013

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

18,596
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

3,160
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

157
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.22,494

Other

Genscan gene predictions107,132