COL6A3 (collagen type VI alpha 3 chain) - Rat Genome Database

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Gene: COL6A3 (collagen type VI alpha 3 chain) Chlorocebus sabaeus
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Symbol: COL6A3
Name: collagen type VI alpha 3 chain
RGD ID: 18795260
Description: ENCODES a protein that exhibits serine-type endopeptidase inhibitor activity (inferred); INVOLVED IN neuron apoptotic process (ortholog); phosphatidylinositol 3-kinase/protein kinase B signal transduction (ortholog); response to glucose (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Ataxia (ortholog); autosomal recessive distal hereditary motor neuronopathy (ortholog); Bethlem myopathy (ortholog); FOUND IN extracellular matrix (ortholog); sarcolemma (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-3(VI) 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
ChlSab1.110123,326,337 - 123,418,836 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10123,327,102 - 123,400,114 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,621 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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


Genomics

Comparative Map Data
COL6A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110123,326,337 - 123,418,836 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10123,327,102 - 123,400,114 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,621 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
COL6A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382237,324,018 - 237,414,164 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2237,324,003 - 237,414,328 (-)EnsemblGRCh38hg38GRCh38
GRCh372238,232,661 - 238,322,807 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362237,897,401 - 237,987,559 (-)NCBINCBI36Build 36hg18NCBI36
Build 342238,014,661 - 238,104,820NCBI
Celera2231,946,425 - 232,036,576 (-)NCBICelera
Cytogenetic Map2q37.3NCBI
HuRef2230,024,688 - 230,114,910 (-)NCBIHuRef
CHM1_12238,238,749 - 238,328,955 (-)NCBICHM1_1
T2T-CHM13v2.02237,815,093 - 237,905,193 (-)NCBIT2T-CHM13v2.0
Col6a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39190,694,582 - 90,771,710 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl190,693,645 - 90,771,693 (-)EnsemblGRCm39 Ensembl
GRCm38190,766,860 - 90,844,001 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl190,765,923 - 90,843,971 (-)EnsemblGRCm38mm10GRCm38
MGSCv37192,663,435 - 92,740,514 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36192,597,264 - 92,674,343 (-)NCBIMGSCv36mm8
MGSCv36191,192,168 - 91,253,776 (-)NCBIMGSCv36mm8
Celera193,712,460 - 93,789,439 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map145.53NCBI
Col6a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8998,809,171 - 98,887,060 (-)NCBIGRCr8
mRatBN7.2991,361,578 - 91,439,434 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl991,361,583 - 91,439,471 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0997,926,784 - 98,004,643 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl997,926,787 - 98,004,546 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0997,607,496 - 97,685,349 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4989,990,129 - 90,043,697 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1990,169,794 - 90,232,286 (-)NCBI
Celera988,906,089 - 88,983,949 (-)NCBICelera
Cytogenetic Map9q36NCBI
Col6a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555422,887,723 - 2,949,062 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555422,869,183 - 2,950,569 (+)NCBIChiLan1.0ChiLan1.0
COL6A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213139,953,644 - 140,044,998 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B139,968,611 - 140,060,569 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B124,554,478 - 124,644,482 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B243,407,786 - 243,497,700 (-)NCBIpanpan1.1PanPan1.1panPan2
COL6A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12547,971,439 - 48,052,673 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2547,971,315 - 48,052,402 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2548,469,819 - 48,549,745 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02548,356,794 - 48,438,226 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2548,356,805 - 48,438,297 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12548,233,582 - 48,313,731 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02548,022,112 - 48,102,355 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02548,253,810 - 48,333,969 (-)NCBIUU_Cfam_GSD_1.0
Col6a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303189,956,267 - 190,034,205 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936525921,725 - 983,377 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936525905,419 - 983,486 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL6A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15137,011,433 - 137,103,709 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115137,011,549 - 137,103,687 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215151,450,581 - 151,542,424 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Col6a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248472,787,319 - 2,863,853 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248472,786,560 - 2,863,800 (-)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 2 1
Low 34 14 41
Below cutoff 4 18

Sequence


RefSeq Acc Id: ENSCSAT00000004181   ⟹   ENSCSAP00000002441
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl10123,327,102 - 123,400,114 (-)Ensembl
RefSeq Acc Id: XM_007966764   ⟹   XP_007964955
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,337 - 123,418,690 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,621 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007966765   ⟹   XP_007964956
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,485 - 123,418,836 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,494 - 76,067,621 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007966766   ⟹   XP_007964957
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,485 - 123,418,681 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,621 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007966767   ⟹   XP_007964958
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,485 - 123,418,680 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,621 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007966768   ⟹   XP_007964959
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,337 - 123,418,690 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,496 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007966769   ⟹   XP_007964960
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,485 - 123,418,676 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,621 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007966770   ⟹   XP_007964961
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.110123,326,337 - 123,418,690 (-)NCBI
Vero_WHO_p1.0NW_02366604075,975,426 - 76,067,496 (+)NCBI
Sequence:
RefSeq Acc Id: XP_007964961   ⟸   XM_007966770
- Peptide Label: isoform X6
RefSeq Acc Id: XP_007964959   ⟸   XM_007966768
- Peptide Label: isoform X4
- UniProtKB: A0A0D9R1F2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007964955   ⟸   XM_007966764
- Peptide Label: isoform X1
- UniProtKB: A0A0D9R1F2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007964956   ⟸   XM_007966765
- Peptide Label: isoform X1
- UniProtKB: A0A0D9R1F2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007964957   ⟸   XM_007966766
- Peptide Label: isoform X2
- UniProtKB: A0A0D9R1F2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007964958   ⟸   XM_007966767
- Peptide Label: isoform X3
- UniProtKB: A0A0D9R1F2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_007964960   ⟸   XM_007966769
- Peptide Label: isoform X5
- UniProtKB: A0A0D9R1F2 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000002441   ⟸   ENSCSAT00000004181


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000006162 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000004181.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
  4.10.410.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  Kunitz_BPTI_sf UniProtKB/TrEMBL
  Prtase_inh_Kunz-CS UniProtKB/TrEMBL
  vWA_collagen_alpha3-VI-like UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report csab:103218151 UniProtKB/TrEMBL
NCBI Gene COL6A3 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-3(VI) CHAIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PRINTS BASICPTASE UniProtKB/TrEMBL
  VWFADOMAIN UniProtKB/TrEMBL
PROSITE BPTI_KUNITZ_1 UniProtKB/TrEMBL
  BPTI_KUNITZ_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART SM00131 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
  SSF57362 UniProtKB/TrEMBL
UniProt A0A0D9R1F2 ENTREZGENE, UniProtKB/TrEMBL