Col25a1 (collagen type XXV alpha 1 chain) - Rat Genome Database

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Gene: Col25a1 (collagen type XXV alpha 1 chain) Chinchilla lanigera
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Symbol: Col25a1
Name: collagen type XXV alpha 1 chain
RGD ID: 9005862
Description: ENCODES a protein that exhibits amyloid-beta binding (ortholog); heparin binding (ortholog); identical protein binding (ortholog); INVOLVED IN axonogenesis involved in innervation (ortholog); ASSOCIATED WITH arthrogryposis multiplex congenita (ortholog); congenital fibrosis of the extraocular muscles 5 (ortholog); genetic disease (ortholog); FOUND IN extracellular region (ortholog); extracellular space (ortholog); plasma membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(XXV) chain; collagen, type XXV, alpha 1
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955496839,561 - 1,250,614 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col25a1Chinchillaarthrogryposis multiplex congenita  ISORGD:16033758554872ClinVar Annotator: match by term: ArthrogryposisClinVarPMID:25741868
Col25a1Chinchillacongenital fibrosis of the extraocular muscles 5  ISORGD:16033758554872ClinVar Annotator: match by term: COL25A1-related condition | ClinVar Annotator: match by term: Fibrosis of more ...ClinVarPMID:25500261|PMID:25741868|PMID:28492532|PMID:31875546
Col25a1Chinchillagenetic disease  ISORGD:16033758554872ClinVar Annotator: match by term: Inborn genetic diseasesClinVar 
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col25a1Chinchillacongenital fibrosis of the extraocular muscles 5  ISORGD:16033757240710 OMIM 


Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col25a1Chinchillaaxonogenesis involved in innervation acts_upstream_of_or_withinISORGD:16214579068941 PMID:24453327MGIPMID:24453327

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col25a1Chinchillaextracellular region located_inISORGD:16033759068941 PMID:11927537MGIPMID:11927537
Col25a1Chinchillaextracellular space located_inISORGD:16033759068941 PMID:11927537UniProtPMID:11927537
Col25a1Chinchillaplasma membrane located_inISORGD:16033759068941 PMID:11927537MGIPMID:11927537

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Col25a1Chinchillaamyloid-beta binding enablesISORGD:16033759068941 PMID:11927537, PMID:15215182, PMID:15522881, PMID:15615705UniProtPMID:11927537|PMID:15215182|PMID:15522881|PMID:15615705
Col25a1Chinchillaheparin binding enablesISORGD:16033759068941 PMID:15522881UniProtPMID:15522881
Col25a1Chinchillaidentical protein binding enablesISOUniProtKB:Q9BXS0-39068941 PMID:15522881IntActPMID:15522881
Col25a1Chinchillaprotein binding enablesISOUniProtKB:A8K2U6|UniProtKB:O14901|UniProtKB:P05067|UniProtKB:P17612|UniProtKB:P37173|UniProtKB:P50454|UniProtKB:P56539|UniProtKB:P63151|UniProtKB:Q9BVL2|UniProtKB:Q9UGJ0|UniProtKB:Q9UJY5-4|UniProtKB:Q9UNE79068941 PMID:32814053IntActPMID:32814053


#
Reference Title
Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species


Col25a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955496839,561 - 1,250,614 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBIChiLan1.0ChiLan1.0
COL25A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384108,808,725 - 109,302,658 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4108,808,725 - 109,302,752 (-)EnsemblGRCh38hg38GRCh38
GRCh374109,729,881 - 110,223,814 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364109,954,421 - 110,443,248 (-)NCBINCBI36Build 36hg18NCBI36
Celera4107,029,732 - 107,518,680 (-)NCBICelera
Cytogenetic Map4q25NCBI
HuRef4105,464,237 - 105,956,593 (-)NCBIHuRef
CHM1_14109,708,453 - 110,200,435 (-)NCBICHM1_1
T2T-CHM13v2.04112,110,611 - 112,604,870 (-)NCBIT2T-CHM13v2.0
Col25a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393129,973,992 - 130,393,533 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3129,925,150 - 130,393,526 (+)EnsemblGRCm39 Ensembl
GRCm383130,180,358 - 130,599,884 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3130,131,501 - 130,599,877 (+)EnsemblGRCm38mm10GRCm38
MGSCv373129,883,796 - 130,299,335 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363130,170,033 - 130,585,572 (+)NCBIMGSCv36mm8
Celera3136,700,003 - 137,111,818 (+)NCBICelera
Cytogenetic Map3G3NCBI
cM Map359.99NCBI
Col25a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82221,429,378 - 221,828,536 (+)NCBIGRCr8
mRatBN7.22218,755,152 - 219,154,348 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2218,755,691 - 219,153,501 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.02235,515,364 - 235,705,448 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2235,596,123 - 235,715,057 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02254,067,074 - 254,256,966 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2211,033,464 - 211,420,527 (+)NCBICelera
Cytogenetic Map2q43NCBI
COL25A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23106,903,996 - 107,403,679 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14107,199,882 - 107,697,183 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04101,311,291 - 101,808,618 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14111,885,022 - 112,378,687 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4111,886,313 - 112,378,062 (-)Ensemblpanpan1.1panPan2
COL25A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13229,119,875 - 29,567,994 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3229,124,996 - 29,567,481 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3212,454,708 - 12,899,162 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03229,350,282 - 29,794,748 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3229,350,312 - 29,794,242 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13229,344,713 - 29,789,307 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03229,089,004 - 29,534,144 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03210,322,491 - 10,767,078 (+)NCBIUU_Cfam_GSD_1.0
Col25a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530111,393,313 - 11,849,115 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936563105,551 - 557,682 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL25A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8112,867,664 - 113,334,097 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18112,866,597 - 113,335,765 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28121,286,327 - 121,453,787 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL25A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1756,730,456 - 57,229,587 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603735,356,307 - 35,872,306 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col25a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624830440,429 - 838,818 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624830440,028 - 842,635 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

.





1 to 17 of 17 rows
RefSeq Transcripts XM_013505431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_013505438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AGCD01062244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AGCD01062251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GBCE01025822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
1 to 17 of 17 rows

Ensembl Acc Id: ENSCLAT00000003897   ⟹   ENSCLAP00000003821
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_004955496839,561 - 1,250,614 (+)Ensembl
Ensembl Acc Id: ENSCLAT00000003898   ⟹   ENSCLAP00000003822
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_004955496839,561 - 1,249,994 (+)Ensembl
RefSeq Acc Id: XM_013505431   ⟹   XP_013360885
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505432   ⟹   XP_013360886
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505433   ⟹   XP_013360887
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505434   ⟹   XP_013360888
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505435   ⟹   XP_013360889
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505436   ⟹   XP_013360890
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505437   ⟹   XP_013360891
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013505438   ⟹   XP_013360892
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBI
Sequence:
1 to 5 of 10 rows
1 to 5 of 10 rows
RefSeq Acc Id: XP_013360886   ⟸   XM_013505432
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_013360889   ⟸   XM_013505435
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_013360885   ⟸   XM_013505431
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_013360887   ⟸   XM_013505433
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_013360888   ⟸   XM_013505434
- Peptide Label: isoform X4
- UniProtKB: A0A8C2UUD7 (UniProtKB/TrEMBL)
- Sequence:



1 to 13 of 13 rows
Database
Acc Id
Source(s)
Ensembl Genes ENSCLAG00000002719 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000003897 ENTREZGENE
  ENSCLAT00000003897.1 UniProtKB/TrEMBL
  ENSCLAT00000003898 ENTREZGENE
  ENSCLAT00000003898.1 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_Structural_Proteins UniProtKB/TrEMBL
NCBI Gene Col25a1 ENTREZGENE
PANTHER COLLAGEN ALPHA-1(XXV) CHAIN UniProtKB/TrEMBL
  SI:CH211-266K2.1 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
UniProt A0A8C2URX0_CHILA UniProtKB/TrEMBL
  A0A8C2UUD7 ENTREZGENE, UniProtKB/TrEMBL
1 to 13 of 13 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Col25a1  collagen type XXV alpha 1 chain    collagen, type XXV, alpha 1  Symbol and/or name change 5135510 APPROVED