XB-FEAT-12564498: Difference between revisions

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=''col11a2''=  
=''col11a2l''=  
This is the community wiki page for the gene ''col11a2''' 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 ''col11a2l'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.


=nomenclature changes=
=nomenclature changes=
01May2023


01MAY2023
''Xenopus'' gene name changed from ''collagen, type XI, alpha 2'' to ''collagen type XI alpha 2 chain'' (removing commas).


''Xenopus'' gene symbol was changed from ''col11a2'' to ''col11a2.2''
03 OCT,2023


''Xenopus'' gene name was changed from ''collagen type XI alpha 2 chain'' to ''collagen type XI alpha 2 chain gene 2''
Gene name was changed from ''collagen type XI alpha 2 chain'' to ''collagen type XI alpha 2 chain like'', following synteny analysis.


=orthology and synteny=
Synteny supports the genes on XB-GENEPAGE-876668 as the true ''col11a2'' orthologs, flanked by ''rxrb'' and ''mhc2-dab'', in ''Xtropicalis'' and ''X. laevis.S'', a pattern shared with Human.  Note: There is no ''Xla.col11a2.L''.
1MAY2023


2 different 'collagen type XI alpha 2 chain' genes are annotated on Chromosome 8 in the v10 ''X. tropicalis'' genome:
Subsequently, this collagen gene is provisionaly called col11a2-like'', a 2nd collagen type 11a2 gene on Chr8, flanked by 'ficolin'' and ''inmt/nntm'' gene strings.


1) GeneID:448277 on this gene page XB-GENEPAGE-12564498
( I am not investigating whether this is indeed a collagen gene, assuming it is) .
Xtr.chr8: ''Loc(ficolin1b)< LOC#(ficolin1b-like)> '''col11a2l>''' X XB5814630(inmt)<  LOC100485680(nnmt)>''
 
Is there a Xlaevis col11a2l.L gene? No, not on chr8L/S, 7L or 5L (see below)
 
=synteny & orthology=


2) GeneID:100488265 (not represented on a Xenbase genepage)  
03 OCT,2023
   
 
True '''''col11a2'''''
 
Xtrop chr8:    syngap1.L<  LOC100486535(unch)  cuta.L>  phf1 < slc39a7 <  hsd17b8> ring1>////  rxrb>  '''col11a2*>'''  mhc2-dcb<  post12< tap1< tap2>
 
  *was col11a2p1- but they are protein coding, not  pseudogenes)  
 
Xla Chr8L:     syngap1.L<    cuta.L>  phf1.L< slc39a7.L<  ring1.L> ///LOC100137644(unch|?hmga2)<  rxrb.L> mhc-dab.L< mhc-daa.L> LOC108719087(p2rx7-like)< mhc2-dcb.L(eladab-a)<  mhc2-dca.L> mhc2-dbb.L<  LOC121397044(unch|)<  LOC121397045<. mhc2-dba
note no Xla.L gene
 
XlaChr8S: slc39a7.S <  hsd17b8> ring1>  rps18.S> wdr46.2> pfdn6.S> tapbp.S<  zbtb22.S< LOC100126628(unch|?hmga2)<  rxrb.S> '''LOC108700220(col11a2.S)'''> brd.S< mhc2-dma.S
 
Human: chr6: BRD2> HLA-DOA<  HLA-DPA1< HLA-DPB1> HLA-DPA2< COL11A2P1< '''COL11A2<'''  RXRB< SLC39A7> RING1>
 
 
'''''col11a2-like'''''


Synteny supports the ''X. tropicalis'' GeneID:448277 as the true ortholog of human COL11A2, as it is flanked by a MHC-gene and ''rxrb'', and X.tropChr8 GeneID:100488265 as a 2nd col11a2 gene.
''Xtrop.chr8: Loc(ficolin1b)< LOC#(ficolin1b-like)> '''col11a2l>''' X XB5814630(inmt)<  LOC100485680(nnmt)>''


Synteny:


HUMAN Chr6: LOC(UNCH)< '''MHC/HLA-DPA3>  HCG24> '''COL11A2'''< RXRB<''' SLC39A7>
''Xla.chr8L: LOC(fcn1-like)< LOC(fcn1-like)<  fcn1.L< fcn1b.L< '''xxxxxxx''' LOC#(inmt#)< LOC#(nnmt#)< LOC#(nnmt)>  LOC#(nnmt)>''
   
X.tropChr8 GeneID:448277: kifcl< mgc147402< '''rxrb> '''col11a2'''> mhc-dab<''' loc100487257<


X.tropChr8 GeneID:100488265:  loc(ficolin1b) loc(ficolin1b-like) '''col11a2.2'''> Xb5814630 loc(inkt) loc(nnmt)
''Xla.chr8S:  tesk1.S> fcn1.S<  LOC108699888(fcn1b)< '''xxxxxxx''' LOC108700639(glutamate) > glul.S> arrdc1.S> ''


''Xla.L chr7L:  nmt.L< LOC#(inmt#)< LOC(znf-mymp1)> LOC#(inmt#)< LOC#(inmt#)< LOC#(inmt#)< LOC#(unch)< LOC#(inmt#)< LOC#(nnmt)>  LOC#(nnmt)> LOC#(unch)< LOC#(unch)< zbtb16.L> LOC#(htr3a) < htr3b.L<''


This indicates the need for nomenclature change for ''X.trop'' GeneID:100488265 from ''col11a2 to col11a2.2'', and a new gene page has been requested) for the ''col11a2.2''.
''Xla.chr5L: tbp.L>  phf10.L> c5h6orf120.L< wdr27> inmt< thbs2.L> ''

Latest revision as of 12:35, 2 October 2023

col11a2l

This is the community wiki page for the gene col11a2l please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

nomenclature changes

01May2023

Xenopus gene name changed from collagen, type XI, alpha 2 to collagen type XI alpha 2 chain (removing commas).

03 OCT,2023

Gene name was changed from collagen type XI alpha 2 chain to collagen type XI alpha 2 chain like, following synteny analysis.

Synteny supports the genes on XB-GENEPAGE-876668 as the true col11a2 orthologs, flanked by rxrb and mhc2-dab, in Xtropicalis and X. laevis.S, a pattern shared with Human. Note: There is no Xla.col11a2.L.

Subsequently, this collagen gene is provisionaly called col11a2-like, a 2nd collagen type 11a2 gene on Chr8, flanked by 'ficolin and inmt/nntm gene strings.

( I am not investigating whether this is indeed a collagen gene, assuming it is) .

Xtr.chr8: Loc(ficolin1b)< LOC#(ficolin1b-like)> col11a2l> X XB5814630(inmt)< LOC100485680(nnmt)>

Is there a Xlaevis col11a2l.L gene? No, not on chr8L/S, 7L or 5L (see below)

synteny & orthology

03 OCT,2023

True col11a2

Xtrop chr8: syngap1.L< LOC100486535(unch) cuta.L> phf1 < slc39a7 < hsd17b8> ring1>//// rxrb> col11a2*> mhc2-dcb< post12< tap1< tap2> 

 *was col11a2p1- but they are protein coding, not  pseudogenes)

Xla Chr8L: syngap1.L< cuta.L> phf1.L< slc39a7.L< ring1.L> ///LOC100137644(unch|?hmga2)< rxrb.L> mhc-dab.L< mhc-daa.L> LOC108719087(p2rx7-like)< mhc2-dcb.L(eladab-a)< mhc2-dca.L> mhc2-dbb.L< LOC121397044(unch|)< LOC121397045<. mhc2-dba 

note no Xla.L gene

XlaChr8S: slc39a7.S < hsd17b8> ring1> rps18.S> wdr46.2> pfdn6.S> tapbp.S< zbtb22.S< LOC100126628(unch|?hmga2)< rxrb.S> LOC108700220(col11a2.S)> brd.S< mhc2-dma.S

Human: chr6: BRD2> HLA-DOA< HLA-DPA1< HLA-DPB1> HLA-DPA2< COL11A2P1< COL11A2< RXRB< SLC39A7> RING1>


col11a2-like

Xtrop.chr8: Loc(ficolin1b)< LOC#(ficolin1b-like)> col11a2l> X XB5814630(inmt)< LOC100485680(nnmt)>


Xla.chr8L: LOC(fcn1-like)< LOC(fcn1-like)< fcn1.L< fcn1b.L< xxxxxxx LOC#(inmt#)< LOC#(nnmt#)< LOC#(nnmt)> LOC#(nnmt)>

Xla.chr8S: tesk1.S> fcn1.S< LOC108699888(fcn1b)< xxxxxxx LOC108700639(glutamate) > glul.S> arrdc1.S>

Xla.L chr7L: nmt.L< LOC#(inmt#)< LOC(znf-mymp1)> LOC#(inmt#)< LOC#(inmt#)< LOC#(inmt#)< LOC#(unch)< LOC#(inmt#)< LOC#(nnmt)> LOC#(nnmt)> LOC#(unch)< LOC#(unch)< zbtb16.L> LOC#(htr3a) < htr3b.L<

Xla.chr5L: tbp.L> phf10.L> c5h6orf120.L< wdr27> inmt< thbs2.L>

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