XB-FEAT-940377

ccnob.4

This is the community wiki page for the gene ccnob.4 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

synteny

long strings CYCLIN-O B and B-like protein coding genes are duplicated in Xenopus tropicalis, but not in similar syntenic regions in mouse or human.

Xtr.Chr8: LOC100486764(phka2l)< LOC108648359(unch)< LOC116406532(ccnopbl)> LOC116406533(ccnopbl)>XB940377> LOC108648361(ncRNA)< LOC116406431(ccnopbl)> phka1< LOCLOC101733971(ccnopb)> LOC101733918(ccnopb)> LOC116406535(ccnopbl)> LOC116406536(ccnopbl)> XB994497(ccnopbl)> LOC116406534(ccnopbl)> cldn2> frmpd3>

Human CHRX: TBC1D8B> RIPPL1< CLDN2> MORC4<

Mouse chrX: tbc1d8b> ripply1< cldn2> morc4< rbm41<

nomenclature changes

This gene is definately a true cyclin gene, an is one of many cyclin o, b or cyclin o, b like genes annotated in 'Xenopus'.

Thus we are provisonally updating its name from unnamed/ XB940377 to cyclin-o- b gene 4, ccnob.4 as it is the 4th (when counting left to right) in this string of 12 duplicated genes. See synteny pattern below.

orthology and homology groups

22MAY2023

Using DIOPT/EGGNOG tool to assess the likely identity of this gene, it matches >2400 proteins from >400 species.

The NCBI refSeq Protein accession for thisX. tropicalis gene matches 17 sequences for X.tropicalis in ENSMBL dtabse:

17 seqs 8364.ENSXETP00000057169, 8364.ENSXETP00000015664, 8364.ENSXETP00000048888, 8364.ENSXETP00000021658, 8364.ENSXETP00000062384, 8364.ENSXETP00000023728, 8364.ENSXETP00000064034, 8364.ENSXETP00000063506, 8364.ENSXETP00000014000, 8364.ENSXETP00000023716, 8364.ENSXETP00000035701, 8364.ENSXETP00000009033, 8364.ENSXETP00000001012, 8364.ENSXETP00000034708, 8364.ENSXETP00000061262, 8364.ENSXETP00000017352, 8364.ENSXETP00000058282 ccni, 8364.ENSXETP00000015664, ccnb3, 8364.ENSXETP00000021658, 8364.ENSXETP00000062384, ccnb2, 8364.ENSXETP00000064034, 8364.ENSXETP00000063506, ccng2, LOC394448, ccnb1.2, ccni2, ccnb1, cntd2, 8364.ENSXETP00000061262, ccng1, ccno

It also matches these Chicken/Gallus proteins: 7 seqs 9031.ENSGALP00000018658, 9031.ENSGALP00000039111, 9031.ENSGALP00000002633, 9031.ENSGALP00000016827, 9031.ENSGALP00000041819, 9031.ENSGALP00000041991, 9031.ENSGALP00000006605 CCNI, CCNI2, CCNG1, CCNG2, CCNB3, CCNO, CCNB2.

and these proteinsin Mouse and rat.

Mus musculus 4 seqs 10090.ENSMUSP00000029270, 10090.ENSMUSP00000058111, 10090.ENSMUSP00000111048, 10090.ENSMUSP00000029368 Ccna2, Ccnjl, Ccnf, Ccna1

Rattus norvegicus 5 seqs 10116.ENSRNOP00000021156, 10116.ENSRNOP00000060445, 10116.ENSRNOP00000039931, 10116.ENSRNOP00000005171, 10116.ENSRNOP00000039779 Ccna2, Ccnf, Ccna1, Ccnjl, Apob

note that: Ccna2, is cylin A2 Ccnf, is cyclin F Ccna1,is cylin A1 Ccng1, i s cyclin G1 Ccno is cyclin O

SO we can confidently say this is another cyclin gene. The cyclins consist of 8 classes of cell cycle regulators, designated A-G, also Q & S in invertebates, that regulate cyclin dependent kinases (CDKs), so further phylogenetic assessment is required to classify this protein.

protein accession

uncharacterized protein LOC100127658 [Xenopus tropicalis]

NCBI Reference Sequence: NP_001106473.2

>NP_001106473.2 uncharacterized protein LOC100127658 [Xenopus tropicalis]

MEILSVGMRKRRREEEEEQEEEIISPGCSPEFKRAKPQGDLRGTSTPTAEEPVPEGEPWNTLTNLADALQ TFREYGEECYLYKKGLEGGYQLENFLENQKDINPTSWNHITTLMINVHRYLRLDFQTLCLGINFLERYVS CTPTNPDTLTRVGATCLYMAYKVAELRYPLPPKLFLPLFDYRMTPAEMRHLERTILRKLLFRLGVPTIDF FLEHFSLLRLTNQEECSPAQLKRAAKSLTAARGIAALCLNQHQDFYMHKPSLMALCCLNVADKIYSYNNP VKVAPTDYPEHQIEECMEKICHLVSIGHYFLHPLLPGVYPAIFPAFNPPTTRPAATPTNQHLPEGRERTP EVASTSRDTAGSQHLEMAERSSHSQDMEGAGYVLHNTYWPTDPYRQVYMHPYMPTPPYWHPYMPPVSYWH PYMHTLPYLHPYGYIFPY