XB-FEAT-6033289: Difference between revisions
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This is the community wiki page for the gene '' | This is the community wiki page for the gene ''xndc1'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
=synteny Xenopus vs Human= | =synteny Xenopus vs Human= | ||
01.01.2021 | |||
the identify of this gene needs further investigation | the identify of this gene needs further investigation | ||
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BLAST alignment of the 2 sequences show no significant similarity so loc100133315 does not represent a duplication of ''trpc2''. | BLAST alignment of the 2 sequences show no significant similarity so loc100133315 does not represent a duplication of ''trpc2''. | ||
=nomenclature changes= | |||
08.19.2021 | |||
this gene/symbol was renamed from ''XB6033289 provisional ortholog of transient receptor potential cation channel, subfamily C, member 2-like (loc100133315)'' to ''Xrcc1 N-terminal domain containing 1 (xndc1)'' following mouse nomenclature, and following recommendations after a review by the NCBIs RefSeq project and HUGO Gene Nomenclature Committee | |||
JIRA reference: HGNC-100. URL: [https://ncbijira.ncbi.nlm.nih.gov/browse/HGNC-100] | |||
They wrote "In vertebrates we've overlooked annotating the XNDC1 gene upstream of TRPC2 due to over-extension of the TRPC2 CDS (PMID: 21854574). The over-extension of the TRPC2 CDS arose in part because these two genes are pseudogenized in human while readthrough transcription occurs in mouse. Below are suggested updates needed for the proper annotation of the XNDC1 gene." | |||
9/17/2021 | |||
Human symbol has changed for genepage ID: 6033289 From xndc1 to XNDC1N | |||
Human symbol has changed for Entrez Gene: 100133315. From LOC100133315 to XNDC1N | |||
Human name has changed for Entrez Gene: 100133315. From XRCC1 N-terminal domain containing 1-like to XRCC1 N-terminal domain containing 1, N-terminal like | |||
Xenopus symbol with remain unchanged at this time. | |||
9/21/2021 | |||
''X. tropicalis'' XNDC1 (GeneID: 100491855, ENSXETG00000003567?, XB-GENE-6033290): Change symbol/name from loc100133315/transient receptor potential cation channel, subfamily C, member 2-like to Xndc1/ Xrcc1 N-terminal domain containing 1 | |||
this gene | |||
22Sept2022 | |||
Human symbol has changed for genepage ID: 6033289 From XNDC1 to XNDC1N | |||
Xenopus symbol was changed for genepage ID: 6033289 From ''xndc1'' to ''xndc1n'' | |||
25April2023''Italic text'' | |||
Xenopus xndc1n versus trpm2 | |||
Again the question arises Has Xb misnamed GeneID:100491855 xndc1n, when Uniprot has the proteins associated wit this gene named ‘short transient receptor potential channel 2’ | |||
DIOPT/EggNog homology search IDs this protein as Xndc1 [now xndc1n, following human update] with very high probability, matching 238 protein in 219 species. | |||
nomenclature stands, Uniprot needs to update protein name. | |||
=Protein= | |||
short transient receptor potential channel 2 isoform X1 [Xenopus tropicalis] | |||
NCBI Reference Sequence: XP_031753282.1 | |||
GenPept Identical Proteins Graphics | |||
>XP_031753282.1 short transient receptor potential channel 2 isoform X1 [Xenopus tropicalis] | |||
MTSLQGGAVRAKNAGNSGIQEVGVRGLARSWAEYPPPMAPITVRHIVSFSSQDPKHPVENLLSEISAQPW | |||
LISPRERGGHLRAELQLEKACHIAYVDIGNCGSAFLQIDVGRSSWPLDRPYVTLLPSTTLMSPADSKQRR | |||
GPNGVRMFKEGDFLVDASAERWDRVRISASQPFNKRDLFGLSFIRFRSALEEEQHEAEGPPPKSEDPKMD | |||
RTPDSETPQLTRGTESRRENPPEGEGQKSQNRLPPSRVPPHTANPACLSRTALMVLTAAKSRKRRFADTT | |||
PPAPPSPHVLGEKSPVPSGSNPAHTPPTPPQKEARNLLGRRRLRMEGPPGRVRARGPERQAAEMGGPPGR | |||
RGHRPRTPRPAGKEQQCSSCPICGGYFQLRYLPSHASTCGEDPPPRVVSLSLSEDSSSSDTDTDIIIPEE | |||
AESWVSCPICSFRFPSNEIEIHANTCGE | |||
Latest revision as of 08:39, 26 April 2023
xndc1
This is the community wiki page for the gene xndc1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
synteny Xenopus vs Human
01.01.2021
the identify of this gene needs further investigation
In X tropicalis v10 genome, the order on Chr2 is: lrif1> <trpc2 <loc100133315 numa1> <il18bp tmem216> <lamtor
trpc2 and loc100133315 models may be non overlapping sequences but of the same allele ( ie together they make full trpc2 sequence)
BLAST alignment of the 2 sequences show no significant similarity so loc100133315 does not represent a duplication of trpc2.
nomenclature changes
08.19.2021
this gene/symbol was renamed from XB6033289 provisional ortholog of transient receptor potential cation channel, subfamily C, member 2-like (loc100133315) to Xrcc1 N-terminal domain containing 1 (xndc1) following mouse nomenclature, and following recommendations after a review by the NCBIs RefSeq project and HUGO Gene Nomenclature Committee
JIRA reference: HGNC-100. URL: [1]
They wrote "In vertebrates we've overlooked annotating the XNDC1 gene upstream of TRPC2 due to over-extension of the TRPC2 CDS (PMID: 21854574). The over-extension of the TRPC2 CDS arose in part because these two genes are pseudogenized in human while readthrough transcription occurs in mouse. Below are suggested updates needed for the proper annotation of the XNDC1 gene."
9/17/2021
Human symbol has changed for genepage ID: 6033289 From xndc1 to XNDC1N
Human symbol has changed for Entrez Gene: 100133315. From LOC100133315 to XNDC1N
Human name has changed for Entrez Gene: 100133315. From XRCC1 N-terminal domain containing 1-like to XRCC1 N-terminal domain containing 1, N-terminal like
Xenopus symbol with remain unchanged at this time.
9/21/2021
X. tropicalis XNDC1 (GeneID: 100491855, ENSXETG00000003567?, XB-GENE-6033290): Change symbol/name from loc100133315/transient receptor potential cation channel, subfamily C, member 2-like to Xndc1/ Xrcc1 N-terminal domain containing 1
22Sept2022
Human symbol has changed for genepage ID: 6033289 From XNDC1 to XNDC1N
Xenopus symbol was changed for genepage ID: 6033289 From xndc1 to xndc1n
25April2023Italic text
Xenopus xndc1n versus trpm2
Again the question arises Has Xb misnamed GeneID:100491855 xndc1n, when Uniprot has the proteins associated wit this gene named ‘short transient receptor potential channel 2’
DIOPT/EggNog homology search IDs this protein as Xndc1 [now xndc1n, following human update] with very high probability, matching 238 protein in 219 species.
nomenclature stands, Uniprot needs to update protein name.
Protein
short transient receptor potential channel 2 isoform X1 [Xenopus tropicalis]
NCBI Reference Sequence: XP_031753282.1
GenPept Identical Proteins Graphics
>XP_031753282.1 short transient receptor potential channel 2 isoform X1 [Xenopus tropicalis] MTSLQGGAVRAKNAGNSGIQEVGVRGLARSWAEYPPPMAPITVRHIVSFSSQDPKHPVENLLSEISAQPW LISPRERGGHLRAELQLEKACHIAYVDIGNCGSAFLQIDVGRSSWPLDRPYVTLLPSTTLMSPADSKQRR GPNGVRMFKEGDFLVDASAERWDRVRISASQPFNKRDLFGLSFIRFRSALEEEQHEAEGPPPKSEDPKMD RTPDSETPQLTRGTESRRENPPEGEGQKSQNRLPPSRVPPHTANPACLSRTALMVLTAAKSRKRRFADTT PPAPPSPHVLGEKSPVPSGSNPAHTPPTPPQKEARNLLGRRRLRMEGPPGRVRARGPERQAAEMGGPPGR RGHRPRTPRPAGKEQQCSSCPICGGYFQLRYLPSHASTCGEDPPPRVVSLSLSEDSSSSDTDTDIIIPEE AESWVSCPICSFRFPSNEIEIHANTCGE