XB-FEAT-5953480: Difference between revisions
| Line 6: | Line 6: | ||
Xenopus '' | Xenopus ''cupin1'' gene is found on chromosome 1/1L/1S in ''Xenopus'', and a 9-exon gene that is473aa in Xenopus)and has a N-terminal CLLAC domain and either a C-terminal bicupin_oxalic or two CUPIN_1 domains. This is the ancestral '''CUPIN1''' gene is found in birds, reptiles, amphibians, mammals and all the way back to sharks like ''Callorhinchus milii''. | ||
NOTE that | NOTE that cupin1 genes are flanked by C18orf54 and RAB27b. | ||
In ''X. tropicali''s and ''X. laevis.L'' subgenome, there is a 2nd duplicated '' | In ''X. tropicali''s and ''X. laevis.L'' subgenome, there is a 2nd duplicated ''cupin1'' gene (we will called it ''cupin1.2'') which also has a 9 exons, and codes for a slightly shorter 471aa protein, and it is absent from Xlaevis S subgenome. Following the synteny pattern for true CUPIN1 orthologs, we have named the gene closest to ''c1h18orf54'' ( the ortholog of C18orf54) ''cupin1'', and the duplicated gene next to ''rab27b, cupin1.2.'' | ||
We take infer that as it has the same 9-exon structure it is a duplicated gene, a common enough occurance in Xenopus. HGNC note that there is often a 2nd 5-exon DYNAP gene or pseudogene in cow, dog, cat, shrew, opossum, and koala, but there is no sign of this shorter gene in the v10 ''Xenopus'' genome annotations. | We take infer that as it has the same 9-exon structure it is a duplicated gene, a common enough occurance in Xenopus. HGNC note that there is often a 2nd 5-exon DYNAP gene or pseudogene in cow, dog, cat, shrew, opossum, and koala, but there is no sign of this shorter gene in the v10 ''Xenopus'' genome annotations. | ||
| Line 16: | Line 16: | ||
synteny patterns: | synteny patterns: | ||
Xtrop: ccdc68> ... rab27b> ... ''' | Xtrop: ccdc68> ... rab27b> ... '''cupin1.2<''' ... LOC116408353(lnRNA)> ... '''cupin1 <''' ... c1h18orf54< ...stard6< | ||
Xla.L: ccdc68.L> ... rab27b.L> ... ''' | Xla.L: ccdc68.L> ... rab27b.L> ... '''cupin1.2.L<''' ... '''cupin1 <''' ... c1h18orf54.L< ...stard6.L< | ||
Xla.L:ccdc68.S> ... rab27b.S> ... ''' | Xla.L:ccdc68.S> ... rab27b.S> ... '''cupin1.s<''' ... c1h18orf54.S< ...stard6.S< | ||
cupin1.2 gene IDs: | |||
Xtrop | Xtrop cupin1.2 NCBI gene ID:100485626 | ||
Xla | Xla cupin1.2.L NCBI gene ID:108695867 | ||
Revision as of 01:29, 14 February 2023
cupin1
This is the community wiki page for the gene cupin1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes and synteny
09FEB2023
Xenopus cupin1 gene is found on chromosome 1/1L/1S in Xenopus, and a 9-exon gene that is473aa in Xenopus)and has a N-terminal CLLAC domain and either a C-terminal bicupin_oxalic or two CUPIN_1 domains. This is the ancestral CUPIN1 gene is found in birds, reptiles, amphibians, mammals and all the way back to sharks like Callorhinchus milii.
NOTE that cupin1 genes are flanked by C18orf54 and RAB27b.
In X. tropicalis and X. laevis.L subgenome, there is a 2nd duplicated cupin1 gene (we will called it cupin1.2) which also has a 9 exons, and codes for a slightly shorter 471aa protein, and it is absent from Xlaevis S subgenome. Following the synteny pattern for true CUPIN1 orthologs, we have named the gene closest to c1h18orf54 ( the ortholog of C18orf54) cupin1, and the duplicated gene next to rab27b, cupin1.2.
We take infer that as it has the same 9-exon structure it is a duplicated gene, a common enough occurance in Xenopus. HGNC note that there is often a 2nd 5-exon DYNAP gene or pseudogene in cow, dog, cat, shrew, opossum, and koala, but there is no sign of this shorter gene in the v10 Xenopus genome annotations.
synteny patterns:
Xtrop: ccdc68> ... rab27b> ... cupin1.2< ... LOC116408353(lnRNA)> ... cupin1 < ... c1h18orf54< ...stard6<
Xla.L: ccdc68.L> ... rab27b.L> ... cupin1.2.L< ... cupin1 < ... c1h18orf54.L< ...stard6.L<
Xla.L:ccdc68.S> ... rab27b.S> ... cupin1.s< ... c1h18orf54.S< ...stard6.S<
cupin1.2 gene IDs:
Xtrop cupin1.2 NCBI gene ID:100485626
Xla cupin1.2.L NCBI gene ID:108695867