XB-FEAT-940377: Difference between revisions
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= | =''ccnob.4''= | ||
This is the community wiki page for the gene '' | 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= | =synteny= | ||
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= | =nomenclature changes= | ||
This gene is definately a cyclin, | 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. | 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= | =orthology and homology groups= | ||
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note that: | note that: | ||
Ccna2, is cylin A2 | Ccna2, is cylin A2 | ||
Ccnf, is cyclin F | Ccnf, is cyclin F | ||
Ccna1,is cylin A1 | Ccna1,is cylin A1 | ||
Ccng1, | |||
Ccng1, is cyclin G1 | |||
Ccno is cyclin O | Ccno is cyclin O | ||
based on these results, we can confidently say this is another 'cyclin gene'. The cyclins consist of 8 classes of cell cycle regulators, designated A-G, also O, Q & S, that regulate cyclin dependent kinases (CDKs). Further phylogenetic assessment is required to fully classify this protein. | |||
=protein accession= | =protein accession= | ||
Latest revision as of 12:02, 22 May 2023
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, is cyclin G1
Ccno is cyclin O
based on these results, we can confidently say this is another 'cyclin gene'. The cyclins consist of 8 classes of cell cycle regulators, designated A-G, also O, Q & S, that regulate cyclin dependent kinases (CDKs). Further phylogenetic assessment is required to fully 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