XB-FEAT-5953480: Difference between revisions

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=''dynap''=  
=''cupin1''=  
This is the community wiki page for the gene ''dynap'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
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=
=nomenclature changes and synteny=
Line 6: Line 6:




Xenopus  ''dynap'' gene is found on chromosome 1/1L/1S in Xenopus, and is the ancestral 9-exon gene that is ~475 aa in all taxa (473aa in Xenopus) and having a N-terminal CLLAC domain and either a C-terminal bicupin_oxalic or two CUPIN_1 domains. This is the ancestral "DYNAP" gene is found in birds, reptiles, amphibians, mammals and all the way back to sharks like ''Callorhinchus milii''.
Xenopus  ''cupin1'' gene is found on chromosome 1/1L/1S in ''Xenopus'', and a 9-exon gene that is 473aa 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 DYNAP genes are flanked by C18orf54 and RAB27b.
NOTE that ''cupin1'' genes are flanked by '''C18orf54 and RAB27b.'''


In ''X. tropicali''s and ''X. laevis.L'' subgenome, there is a 2nd duplicated ''dynap'' gene (we will called it ''dynap.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 DYNAP orthologs, we have named the gene closest to  ''c1h18orf54'' ( the ortholog of C18orf54) ''dynap'', and the duplicated gene next to ''rab27b, dynap.2.''
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 the ''X. laevis S'' subgenome.  


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.  
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'', as  ''cupin1.2.''
 
We inferred 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:
synteny patterns:


Xtrop: ccdc68> ... rab27b> ... '''dynap.2<''' ... LOC116408353(lnRNA)> ... '''dynap<''' ... c1h18orf54< ...stard6<
Xtrop: ccdc68> ... rab27b> ... '''cupin1.2<''' ... LOC116408353(lnRNA)> ... '''cupin1 <''' ... c1h18orf54< ...stard6<


Xla.L: ccdc68.L> ... rab27b.L> ... '''dynap.2.L<''' ... '''dynap<''' ... c1h18orf54.L< ...stard6.L<
Xla.L: ccdc68.L> ... rab27b.L> ... '''cupin1.2.L<''' ... '''cupin1 <''' ... c1h18orf54.L< ...stard6.L<


Xla.L:ccdc68.S> ... rab27b.S> ... '''dynap.S<''' ... c1h18orf54.S< ...stard6.S<
Xla.L:ccdc68.S> ... rab27b.S> ... '''cupin1.s<''' ... c1h18orf54.S< ...stard6.S<




dynap.2 gene IDs:
cupin1.2 gene IDs:


Xtrop dynap.2 NCBI gene ID:100485626
Xtrop cupin1.2 NCBI gene ID:100485626


Xla dynap.2.L  NCBI gene ID:108695867
Xla cupin1.2.L  NCBI gene ID:108695867

Latest revision as of 10:53, 15 June 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 is 473aa 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 the X. laevis 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, as cupin1.2.

We inferred 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

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