XB-FEAT-29071333: Difference between revisions
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=''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 | |||
As 'atrx2' gene symbol is not used anywhere else, I am changing it to ''atrxl' (another like gene) and removing the human orthologs from the 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 | |||
=synteny patterns= | =synteny patterns= | ||
Revision as of 12:46, 8 June 2023
atrx2
This is the community wiki page for the Xenopus atrx2 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
As 'atrx2' gene symbol is not used anywhere else, I am changing it to atrxl' (another like gene) and removing the human orthologs from the 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