XB-FEAT-29089670: Difference between revisions
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=parp14l.2= | =''parp14l.2''= | ||
=nomenclature changes= | =nomenclature changes= | ||
21FEB2025 | 21FEB2025 | ||
following review by David Webb at NCBI, RSCOM-838 XB-GENEPAGE-29091266 and XB-GENEPAGE-6458584 both named ''parp14.3'', synteny for these genes and symbol clash with ''parp14'' genes on Chr1, the following notes and changes have been made. | following review by David Webb at NCBI, RSCOM-838 XB-GENEPAGE-29091266 and XB-GENEPAGE-6458584 both named ''parp14.3'', synteny for these genes and symbol clash with ''parp14'' genes on Chr1, the following notes and changes have been made. | ||
RSCOM-838 XB-GENEPAGE-29091266 and XB-GENEPAGE-6458584 both named parp14.3 | RSCOM-838 XB-GENEPAGE-29091266 and XB-GENEPAGE-6458584 both named parp14.3 | ||
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Given synteny evidence, we consider this the true tandem duplication series, ''parp14'' being represented on XB-GENEPAGE-29091266. and others | Given synteny evidence, we consider this the true tandem duplication series, ''parp14'' being represented on XB-GENEPAGE-29091266. and others | ||
Considering that a) the genes on chr1/1L (not 9/9_10L) b) the protein is not found/characterized in EggNogg6.0 and thus has no previously identified homology group, and 3) NCBI machine annotation considered them to be ''parp14'' genes, we have changed nomenclature to ''parp14l'' , and ''parp14l.2'' to indicate the '''lack''' the shared synteny and that these genes may be/likely are a ''Xenopus-specific duplication/translocation'' of ''parp14''. | |||
XB-GENEPAGE-6458584, now has Xtrop XB-GENE-29089671 parp14l (gene ID: 105947701, ''poly(ADP-ribose) polymerase family member 14 like gene 1'' and Xlaevis XB-GENE-29089672 parp14l.L (geneID: 108695267, 'poly(ADP-ribose) polymerase family member 14 like gene 1 L homeolog'') | XB-GENEPAGE-6458584, now has Xtrop XB-GENE-29089671 parp14l (gene ID: 105947701, ''poly(ADP-ribose) polymerase family member 14 like gene 1'' and Xlaevis XB-GENE-29089672 parp14l.L (geneID: 108695267, 'poly(ADP-ribose) polymerase family member 14 like gene 1 L homeolog'') | ||
XB-GENEPAGE-29089670 now has Xtr.parp14l.2, (geneID:105947701)'poly(ADP-ribose) polymerase family member 14 like gene 2'' and Xla.parp14l.2.L (GeneID:108695267) 'poly(ADP-ribose) polymerase family member 14 like gene 2 L homeolog]''. | XB-GENEPAGE-29089670 now has Xtr.parp14l.2, (geneID:105947701)'poly(ADP-ribose) polymerase family member 14 like gene 2'' and Xla.parp14l.2.L (GeneID:108695267) 'poly(ADP-ribose) polymerase family member 14 like gene 2 L homeolog]''. | ||
Latest revision as of 11:43, 21 February 2025
parp14l.2
nomenclature changes
21FEB2025
following review by David Webb at NCBI, RSCOM-838 XB-GENEPAGE-29091266 and XB-GENEPAGE-6458584 both named parp14.3, synteny for these genes and symbol clash with parp14 genes on Chr1, the following notes and changes have been made.
RSCOM-838 XB-GENEPAGE-29091266 and XB-GENEPAGE-6458584 both named parp14.3
2 Xenbase genepage's with identical parp14.3 symbols but distinct gene names: XB-GENEPAGE-29091266/'protein mono-ADP-ribosyltransferase PARP14, gene 3' and XB-GENEPAGE-6458584/'poly (ADP-ribose) polymerase family, member 14, gene 3'.
XB-GENEPAGE-29091266 is on chr 9 and that block of parp14-like genes shares better synteny with the PARP14 genes of other tetrapods (see attached PARP14.docx) so I'd prefer to keep parp14.3 there.
XB-GENEPAGE-6458584 and the adjacent gene on chr 1 are also parp14-like but lack the shared synteny and may be a Xenopus-specific duplication/translocation. Can you retain XB-GENEPAGE-29091266 as parp14.3 and name XB-GENEPAGE-6458584 something else?
Xenbase notes:
Xenopus has 6 duplicate parp14 genes in both X. tropicalis [chr9] and X. laevis [chr9_10L] Given synteny evidence, we consider this the true tandem duplication series, parp14 being represented on XB-GENEPAGE-29091266. and others
Considering that a) the genes on chr1/1L (not 9/9_10L) b) the protein is not found/characterized in EggNogg6.0 and thus has no previously identified homology group, and 3) NCBI machine annotation considered them to be parp14 genes, we have changed nomenclature to parp14l , and parp14l.2 to indicate the lack the shared synteny and that these genes may be/likely are a Xenopus-specific duplication/translocation of parp14.
XB-GENEPAGE-6458584, now has Xtrop XB-GENE-29089671 parp14l (gene ID: 105947701, poly(ADP-ribose) polymerase family member 14 like gene 1 and Xlaevis XB-GENE-29089672 parp14l.L (geneID: 108695267, 'poly(ADP-ribose) polymerase family member 14 like gene 1 L homeolog)
XB-GENEPAGE-29089670 now has Xtr.parp14l.2, (geneID:105947701)'poly(ADP-ribose) polymerase family member 14 like gene 2 and Xla.parp14l.2.L (GeneID:108695267) 'poly(ADP-ribose) polymerase family member 14 like gene 2 L homeolog].