COL5A1 (collagen type V alpha 1 chain) - Rat Genome Database

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Gene: COL5A1 (collagen type V alpha 1 chain) Chlorocebus sabaeus
Analyze
Symbol: COL5A1
Name: collagen type V alpha 1 chain
RGD ID: 18559904
Description: ENCODES a protein that exhibits heparin binding (ortholog); INVOLVED IN blood vessel development (ortholog); collagen fibril organization (ortholog); heart morphogenesis (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH 17-beta hydroxysteroid dehydrogenase 3 deficiency (ortholog); Adams-Oliver Syndrome 5 (ortholog); Animal Mammary Neoplasms (ortholog); FOUND IN basement membrane (inferred); collagen trimer (inferred); collagen type V trimer (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(V) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,301,643 - 3,507,300 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl123,301,175 - 3,459,607 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660581,612,962 - 1,827,783 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
COL5A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,301,643 - 3,507,300 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl123,301,175 - 3,459,607 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660581,612,962 - 1,827,783 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
COL5A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389134,641,803 - 134,844,843 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9134,641,803 - 134,844,843 (+)EnsemblGRCh38hg38GRCh38
GRCh379137,533,649 - 137,736,689 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369136,673,473 - 136,876,510 (+)NCBINCBI36Build 36hg18NCBI36
Build 349134,759,596 - 134,960,684NCBI
Celera9108,048,806 - 108,251,522 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9106,996,262 - 107,200,594 (+)NCBIHuRef
CHM1_19137,682,127 - 137,886,117 (+)NCBICHM1_1
T2T-CHM13v2.09146,859,174 - 147,065,950 (+)NCBIT2T-CHM13v2.0
Col5a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39227,776,393 - 27,929,522 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl227,776,437 - 27,929,526 (+)EnsemblGRCm39 Ensembl
GRCm38227,886,381 - 28,039,510 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl227,886,425 - 28,039,514 (+)EnsemblGRCm38mm10GRCm38
MGSCv37227,741,945 - 27,895,030 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36227,708,694 - 27,859,533 (+)NCBIMGSCv36mm8
Celera227,589,197 - 27,742,307 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Col5a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,606,475 - 31,755,097 (+)NCBIGRCr8
mRatBN7.2311,208,429 - 11,356,715 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,208,512 - 11,354,588 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,276,142 - 14,421,992 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0322,861,404 - 23,007,143 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,115,526 - 21,261,367 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,430,180 - 6,581,010 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,430,201 - 6,578,882 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,788,675 - 11,937,880 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,826,169 - 6,971,054 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.136,826,468 - 6,971,354 (+)NCBI
Celera36,002,130 - 6,146,263 (+)NCBICelera
Cytogenetic Map3p12NCBI
Col5a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555133,533,614 - 3,658,161 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555133,533,612 - 3,660,605 (+)NCBIChiLan1.0ChiLan1.0
COL5A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2114,523,306 - 4,731,588 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan194,525,346 - 4,733,918 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09105,746,388 - 105,956,280 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19134,391,081 - 134,543,769 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9134,342,955 - 134,544,651 (+)Ensemblpanpan1.1panPan2
COL5A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1950,706,852 - 50,856,691 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl950,770,277 - 50,854,728 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,989,837 - 50,140,047 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0951,583,512 - 51,733,920 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl951,583,513 - 51,732,204 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1950,343,968 - 50,494,164 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0950,687,121 - 50,838,052 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0950,765,252 - 50,915,697 (+)NCBIUU_Cfam_GSD_1.0
Col5a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947200,761,510 - 200,900,677 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366692,476,818 - 2,580,891 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366692,474,381 - 2,613,541 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL5A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1273,971,971 - 274,085,111 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11273,934,219 - 274,083,264 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21308,064,240 - 308,174,334 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Col5a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247602,593,961 - 2,713,772 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247602,593,923 - 2,713,772 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system hemolymphoid system nervous system
High
Medium 24 32
Low 12 16 28
Below cutoff 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000013698   ⟹   ENSCSAP00000011688
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl123,301,175 - 3,459,607 (-)Ensembl
RefSeq Acc Id: XM_037986995   ⟹   XP_037842923
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_0236660581,612,962 - 1,827,783 (+)NCBI
Protein Sequences
Protein RefSeqs XP_037842923 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000011688.1
Reference Protein Sequences
RefSeq Acc Id: ENSCSAP00000011688   ⟸   ENSCSAT00000013698
RefSeq Acc Id: XP_037842923   ⟸   XM_037986995
- UniProtKB: A0A0D9RSU9 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000015604 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000013698.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
NCBI Gene COL5A1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(V) CHAIN UniProtKB/TrEMBL
Pfam COLFI UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
PROSITE NC1_FIB UniProtKB/TrEMBL
SMART COLFI UniProtKB/TrEMBL
UniProt A0A0D9RSU9 ENTREZGENE, UniProtKB/TrEMBL