Ensembl mobile site help

Things to know when navigating the Ensembl mobile site

Search box

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more.

Top navigation

Touch MENU button to open the main menu and touch again to close.

Touch MENU

Left hand side menu

Touch the left menu icon () or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close.

The ? icon

Touch the icon to get help

And don't forget to send us your comments using the feedback link inside the main menu.

EnsemblEnsembl Home

Big-finned mudskipper assembly and gene annotation

Assembly

The PM.fa assembly was submitted by BGI-shenzhen on December 2014. The assembly is on scaffold level, consisting of 76,770 contigs assembled into 26,060 scaffolds. 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 28,254 while the scaffold N50 is 296,161.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000787105.1

Gene annotation

Periophthalmus is a genus of fish in the family Gobiidae, commonly known as mudskippers, native to the mangrove forests along the coasts of Africa, India and Southern Asia. All species under the genus are aggressive and territorial.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyPM.fa, INSDC Assembly GCA_000787105.1, Dec 2014
Base Pairs701,696,780
Golden Path Length701,696,780
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes22,256
Non coding genes1,901
Small non coding genes1,883
Long non coding genes2
Misc non coding genes16
Pseudogenes40
Gene transcripts32,012

Other

Genscan gene predictions44,626

About this species