XB-FEAT-969180

ppp1r3c

This is the community wiki page for the gene ppp1r3c please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase

nomenclature update

7.13.21

The name of this gene was updated to more accurately reflect it orthology to the human gene. It was changed from protein phosphatase 1, regulatory (inhibitor) subunit 3C gene 1 (ppp1r3c.1) to protein phosphatase 1, regulatory (inhibitor) subunit 3C.

gene pattern in Xtrop Chr7: pcgf5> ... hectd2> ...." ppp1r3c1<" ...tnks2> ... fgfbp3< ...drd1c<

Note that it is not on the same chromosome as XB-GENE-876322 (ppp1r3c.2), nor is not immediately adjacent ppp1r3c.2 , so doesn't fit our 'gene 1 gene 2' nomenclature rule for duplications. Note that ppp1r3c.2 gene name/symbol has changed to ppp1r3c2 ( see https://ncbijira.ncbi.nlm.nih.gov/browse/RSCOM-124 for details)

XB-GENE-969181 (XB-GENEPAGE-969180) is the ortholog of the mammalian PPP1R3C gene which also resides at HECTD2>...PPP1R3C<...TNKS2> all the way back to at least gnathostomes.

Zfin calls this gene ppp1r3cb (and NCBI has propagated the ppp1r3cb symbol throughout actinopterygii and chondrichthyes).

RefSeq curator David Webb recommends to name it ppp1r3c so the orthology to human/mouse PPP1R3C is clear and the orthology to "fish" ppp1r3cb is clearer too.

Searches of google and pubmed indicate the symbol ppp1r3c1 has been used just once in an unpublished 2012 thesis on human genes so using that symbol has no significant conflicts.

synteny notes

There are 2 different ‘ppp1r3c’ genes in Xenopus.

XB-GENEPAGE-969180 ppp1r3c gene 1 is on Chromosome 7 in X tropicalis and X. laevis, and it appears to be the true ortholog of human PPP1R3C, as evidenced from synteny /conserved order pattern, being flanked by pcgf5, hectd2 and tnks2 genes across taxa.

synteny pattern

Xenopus: ankrd1 … pcgf5 … hectd2. … ppp1r3c.1 …tnks2 … fgfbp3. … drd1c … tbc1d12

Mouse: Hectd4 … hectd2os … Ppp1r3c< … LOC115489052< … Tnks2> ….

Human: HECTD4-AS1 … PPP1R3C … gapdh28 … LOC107984253 … FAF2P1 …TNKS-DT

Zebrafish chr12: lrp2b> … mpp3b> … ppp1r3cb> … hectd2< … pcgf5b<

Chicken: LOC> … LOC< … … hectd2> … ppp1r3c< tnks2> LOC#<

XB-GENEPAGE-876321 pp1r3c gene 2 is on Chromosome 3 in X. tropicalis and X laevis.

synteny pattern:

Xtr Chr3: chmp7… gins4 … ppp1r3c.2 … gpat4 … loc#1628 … inppa5a.2> … nkx6-3< ank1

MOUSE chr8: ank1> nkx6-3> gpat4< Gins4<. Gm39141> Golga7< Gm24335 (reversed)

Rat chr16: Loc# > … Golga7> … Gins4> … Gpat4> Nxk6-3<

HUMAN chr8: GINS4> … GPAT4-AS1< … GPAT4 > … NKX6-3< … ANK1< …

Zfish chr8: ardis5a> … cox5bb< …gins4> ... ppp1r3c2b>... phyhip

chick chr22: sfrp1< … golga7> … gins4>... ppp1rl> ... gpat4>... nkx6-3

In ‘pp1r3c gene 2’ case, there does not appear to be a syntenic PPP1R3C gene in humans, rat or mouse, but there are ppp1r* genes in zebrafish and chicken.

The orthologs for zebrafish (geneID: 406459) and chicken (gene ID: 395787) have been updated with these ggen IDS on XB-GENEPAGE-876321.

The question is then, are the human and mouse PPP1R3C genes still the orthologs of pp1r3c gene 2, or not?