XB-FEAT-29071333: Difference between revisions
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='' | =''atrxl''= | ||
This is the community wiki page for the'' Xenopus'' '' | This is the community wiki page for the'' Xenopus'' ''atrxl'' genes. Please feel free to record here any relvant information that is not recorded elsewhere on Xenbase. | ||
=''Xenopus artx'' genes= | =''Xenopus artx'' genes= | ||
There are 2 different atrx genes identified in Xenopus v10 assembly. | There are 2 different 'atrx' genes identified in ''Xenopus'' v10 assembly. | ||
''atrx, ATRX chromatin remodeler'' gene on XB-GENEPAGE-980567 for Xtropicalis and Xlaevis L and S subgenomes all on Chr8/8L/8S | ''atrx, ATRX chromatin remodeler'' gene on XB-GENEPAGE-980567 for Xtropicalis and Xlaevis L and S subgenomes all on Chr8/8L/8S | ||
''atrx2, ATRX chromatin remodeler'' on XB-GENEPAGE-29071333 which | ''atrx2, ATRX chromatin remodeler'' on XB-GENEPAGE-29071333 which currently only has a X.laevis.L gene model on Chr1L | ||
atrx genes are | atrx genes on XB-GENEPAGE-980567 are accepted as the true orthologs to Human ATRX, as recognized by NCBi and support by synteny. | ||
* Xtr chr8 klf4a< fgf16> '''atrx'''< magt1< cox7b> atp7a> | |||
* Human chrX: FGF16> '''ATRX'''< MAGT1< COX7B < ATP7A< | |||
= | |||
The identify of ‘atrx2’ is however unclear. | |||
Synteny does NOT indicate any similarly positioned/named gene in other species or human: | |||
* Xla chr1L: abcg2.L> pkd.L< '''atrx2.L<''' ibsp.L< LOC> dspp.L< | |||
* HUMAN CHR4: NUDT9> SPARCL1< DSPP> DMP1> IBSP> MEPE> SPP1> PKD2> | |||
Protein alignment in DIOPT/EggNog to look for homology groups is inconclusive- with only 2 matched with very low confidence scores. BLAST does not identif any other sugnificant results | |||
=nomenclature changes= | |||
07 JUNE 2023 | |||
As 'atrx2' gene symbol is not used anywhere else, I am changing gene symbol from ''atrx2'' to ''atrxl' (another like gene) | |||
THis gene is not a true ortholog of Human ATRX, so I am also removing all orthologs from this gene page. | |||
=Protein= | |||
transcriptional regulator ATRX homolog [Xenopus laevis] | |||
NCBI Reference Sequence: XP_018107822.1 | |||
>XP_018107822.1 transcriptional regulator ATRX homolog [Xenopus laevis] | |||
MVFTQKMKTVLLFVCLFGIAFAYSNSSSSESSESSKSDSSDSSSEENQTAGPVVTAKRLSNLRGDSYRPRRDLLLNLLKRDLKGKKRGSSSSSDEDSTTHSEDRSAVTKSTSTHSHSSESSEEHTNPTLQKVAFTPEPNTSEESSEERTTKLPIV | |||
Latest revision as of 12:39, 5 July 2023
atrxl
This is the community wiki page for the Xenopus atrxl genes. Please feel free to record here any relvant information that is not recorded elsewhere on Xenbase.
Xenopus artx genes
There are 2 different 'atrx' genes identified in Xenopus v10 assembly.
atrx, ATRX chromatin remodeler gene on XB-GENEPAGE-980567 for Xtropicalis and Xlaevis L and S subgenomes all on Chr8/8L/8S
atrx2, ATRX chromatin remodeler on XB-GENEPAGE-29071333 which currently only has a X.laevis.L gene model on Chr1L
atrx genes on XB-GENEPAGE-980567 are accepted as the true orthologs to Human ATRX, as recognized by NCBi and support by synteny.
- Xtr chr8 klf4a< fgf16> atrx< magt1< cox7b> atp7a>
- Human chrX: FGF16> ATRX< MAGT1< COX7B < ATP7A<
The identify of ‘atrx2’ is however unclear.
Synteny does NOT indicate any similarly positioned/named gene in other species or human:
- Xla chr1L: abcg2.L> pkd.L< atrx2.L< ibsp.L< LOC> dspp.L<
- HUMAN CHR4: NUDT9> SPARCL1< DSPP> DMP1> IBSP> MEPE> SPP1> PKD2>
Protein alignment in DIOPT/EggNog to look for homology groups is inconclusive- with only 2 matched with very low confidence scores. BLAST does not identif any other sugnificant results
nomenclature changes
07 JUNE 2023
As 'atrx2' gene symbol is not used anywhere else, I am changing gene symbol from atrx2 to atrxl' (another like gene)
THis gene is not a true ortholog of Human ATRX, so I am also removing all orthologs from this gene page.
Protein
transcriptional regulator ATRX homolog [Xenopus laevis]
NCBI Reference Sequence: XP_018107822.1
>XP_018107822.1 transcriptional regulator ATRX homolog [Xenopus laevis] MVFTQKMKTVLLFVCLFGIAFAYSNSSSSESSESSKSDSSDSSSEENQTAGPVVTAKRLSNLRGDSYRPRRDLLLNLLKRDLKGKKRGSSSSSDEDSTTHSEDRSAVTKSTSTHSHSSESSEEHTNPTLQKVAFTPEPNTSEESSEERTTKLPIV