Difference between revisions of "XB-FEAT-22249066"

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Revision as of 19:41, 28 July 2020

accsl1

Feel free to record here any information now represented elsewhere on Xenbase.

This new genepage was created following a review of astacin-like metalloproteinase genes. See RSCOM-64 and RS-COM50 in RefSeq Communication/JIRA for full discussion.

There's a tandem pair of genes that are common to tetrapods but have been lost in mammals.

Their gene order is fairly well-conserved so orthology across tetrapods is easy to establish.

The general gene order in coelocanth, caecilians and ancestral reptiles is <CRY2 <SLC35C1 CHST1> <TMEM263L *1> <*2 SYT13> <PRDM11.

Frogs have broken synteny on one end of this chr 4 gene block: <ACCS <?? *1> <*2 SYT13> <PRDM11.

Birds have broken this synteny block in two: <CRY2 <SLC35C1 CHST1> <TMEM263L *1> and <*2 SYT13> <PRDM11.

Placental mammals have lost these two genes and TMEM263L but otherwise they retain the gene synteny of <CRY2 <SLC35C1 CHST1> SYT13> <PRDM11.

nomenclature updates

Summary, dated July 2020

Entrez GeneID: 100495810 was determined as not accs ( as it was originally annotated) but rather is a tandem astacin-like gene.

The true X.tropicalis accs gene is the upstream gene GeneID: 101731157.

True accs1 and accs2 genes are lost in mammals and this gene block arose after sarcopterygians split from actinoptyergians.

Unfortunately these tandem astacin-like genes are equally distant to 10 or so fish astacin-like paralogs so it'll be very difficult to establish orthology to zebrafish genes.

So, it falls to CGNC and XenBase to devise a shared nomenclature for these two genes. We propose accs-like gene 1 (accsl1) (temp name/symbol) for Entrez GeneID: 100495810, and accs-like gene 2 (accsl2) (temp name/symbol) GeneID: 100496122, which was previously called syt13.