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 relevant to these genes that is not found elsewhere on Xenbase. | |||
=nomenclature changes= | =nomenclature changes= | ||
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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 10:03, 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)