XB-FEAT-22069202: Difference between revisions

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=''vgf''=
=''vgf''=
This is the community wiki page for the ''Xenopus vgf'' genes. Please feel free to enter here any information relevent to these genes that is not found elsewhere on Xenbase.
This is the community wiki page for the ''Xenopus vgf'' genes. Please feel free to enter here any information relevant to these genes that is not found elsewhere on Xenbase.


=nomenclature changes=
=nomenclature changes=
Line 6: Line 6:
16MAY2023
16MAY2023


Xenopus gene was renamed, changing from ''sprr3, small proline rich protein 3''  to ''vgf , VGF nerve growth factor inducible''.
''Xenopus'' gene was renamed, changing from ''sprr3, small proline rich protein 3''  to ''vgf , VGF nerve growth factor inducible''.
 
 
Changed XB-GENE-22069203 Xtr Gene ID: 105945420 from sprr3 to vgf as
 
1)  NCBIi recognizes it as the ortholog of human VGF
 
2) supported by synteny, with conserved flanking genes ''serpine1'' and  ''ap1s1'' upstream and ''nat16'' (plus duplicates) downstream.
 
=SYNTENY PATTERNS=
 
HumanChr1:  SPRR4> SPRR1A> '''SPRR3'''> LOC(ncRNA)> SPRR1B> SPRR2D< SPRR2A< SPRR2B
 
Note: NO Xenopus genes have been characterised as SPRR# orthologs
 
 
'''Synteny is conserved between Human and Xenopus'''
 
HumanCHR7: TRIM56> SERPINE1> AP1s1> '''VGF'''<  NAT16<  MOGAT3< PLOD3< ZNHITI> CLDN15>
 
Xtrop.v9.1 scff48:    ''nat16>  XB5892957(unch) > [tRNAs] '''vgf'''> ap1s1<  [trnas] serpin1< LOC100495872''
 
Xtrop.v10.Chr3:  ''LOC116409833(muc3)>  serpine1>  ap1s1> '''vgf>'''  [tRNAs] XB5892957(unch? nat.14)> LOC100495706(nat16.13)>  LOC116409835(nat-like.12)< XB5762451(nat.11)< LOC116409834(nat-like.10)< LOC100490742(nat-like.9)<  LOC100490911(nat-like.8) XB5761890(nat16.7)< LOC116409523 (nat-like.6)< LOC116409836(nat-like.5)<  LOC100490569(nat.4) <  LOC101730755(nat.3)< LOC100491420(nat.2)<  nat16<  mogat3< mogat2.1<''
 
Xla.chr3L:  serpine1.L>  ap1s1.L> LOC108711739(vgf)>    LOC108711740(nat16)< LOC108710379(nat)< LOC108711741(nat)< LOC108711742(nat)<  LOC108710380(nat16)< LOC108710381(nat16-p)< LOC108710382(nat16p)<  LOC121393059(natlike) LOC121401654(natike) < LOC121401655(lncRNA)< nat16.L< <  mogat3.L< mogat2.1.L<
 
Xla.chr3S:  serpine1.S>  ap1s1.S> '''LOC108703510(vgf)>'''    LOC108703511(nat16.5)< LOC108703512(nat16.4)< XB5761890.S(nat16.3)< LOC108703513(nat16.2)< LOC121402082(ncRNA)<  LOC108703454(unch/nat16.1?)< LOC108703514(mblac1 like)> LOC733301(tmem4l6m5.1) LOC108703455(tmem4l6m5.2)>  LOC108703456(tmem4l6m5.3)>  lamtor4.S> LOC108703516(trappc14)

Latest revision as of 11:03, 16 May 2023

vgf

This is the community wiki page for the Xenopus vgf genes. Please feel free to enter here any information relevant to these genes that is not found elsewhere on Xenbase.

nomenclature changes

16MAY2023

Xenopus gene was renamed, changing from sprr3, small proline rich protein 3 to vgf , VGF nerve growth factor inducible.


Changed XB-GENE-22069203 Xtr Gene ID: 105945420 from sprr3 to vgf as

1) NCBIi recognizes it as the ortholog of human VGF

2) supported by synteny, with conserved flanking genes serpine1 and ap1s1 upstream and nat16 (plus duplicates) downstream.

SYNTENY PATTERNS

HumanChr1: SPRR4> SPRR1A> SPRR3> LOC(ncRNA)> SPRR1B> SPRR2D< SPRR2A< SPRR2B

Note: NO Xenopus genes have been characterised as SPRR# orthologs


Synteny is conserved between Human and Xenopus

HumanCHR7: TRIM56> SERPINE1> AP1s1> VGF< NAT16< MOGAT3< PLOD3< ZNHITI> CLDN15>

Xtrop.v9.1 scff48: nat16> XB5892957(unch) > [tRNAs] vgf> ap1s1< [trnas] serpin1< LOC100495872

Xtrop.v10.Chr3: LOC116409833(muc3)> serpine1> ap1s1> vgf> [tRNAs] XB5892957(unch? nat.14)> LOC100495706(nat16.13)> LOC116409835(nat-like.12)< XB5762451(nat.11)< LOC116409834(nat-like.10)< LOC100490742(nat-like.9)< LOC100490911(nat-like.8) XB5761890(nat16.7)< LOC116409523 (nat-like.6)< LOC116409836(nat-like.5)< LOC100490569(nat.4) < LOC101730755(nat.3)< LOC100491420(nat.2)< nat16< mogat3< mogat2.1<

Xla.chr3L: serpine1.L> ap1s1.L> LOC108711739(vgf)> LOC108711740(nat16)< LOC108710379(nat)< LOC108711741(nat)< LOC108711742(nat)< LOC108710380(nat16)< LOC108710381(nat16-p)< LOC108710382(nat16p)< LOC121393059(natlike) LOC121401654(natike) < LOC121401655(lncRNA)< nat16.L< < mogat3.L< mogat2.1.L<

Xla.chr3S: serpine1.S> ap1s1.S> LOC108703510(vgf)> LOC108703511(nat16.5)< LOC108703512(nat16.4)< XB5761890.S(nat16.3)< LOC108703513(nat16.2)< LOC121402082(ncRNA)< LOC108703454(unch/nat16.1?)< LOC108703514(mblac1 like)> LOC733301(tmem4l6m5.1) LOC108703455(tmem4l6m5.2)> LOC108703456(tmem4l6m5.3)> lamtor4.S> LOC108703516(trappc14)