COL6A6 (collagen type VI alpha 6 chain) - Rat Genome Database

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Gene: COL6A6 (collagen type VI alpha 6 chain) Canis lupus familiaris
Analyze
Symbol: COL6A6
Name: collagen type VI alpha 6 chain
RGD ID: 12239267
Description: ENCODES a protein that exhibits extracellular matrix structural constituent conferring tensile strength (inferred); ASSOCIATED WITH alkaptonuria (ortholog); genetic disease (ortholog); immunodeficiency 21 (ortholog); FOUND IN collagen-containing extracellular matrix (inferred); extracellular matrix (inferred); extracellular region (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-6(VI) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12327,759,707 - 27,900,971 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2327,759,103 - 27,900,154 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2327,732,899 - 27,874,490 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02328,265,749 - 28,407,486 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2328,265,670 - 28,407,244 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12327,960,796 - 28,102,441 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02328,016,442 - 28,158,900 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02328,271,892 - 28,414,438 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
COL6A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12327,759,707 - 27,900,971 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2327,759,103 - 27,900,154 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2327,732,899 - 27,874,490 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02328,265,749 - 28,407,486 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2328,265,670 - 28,407,244 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12327,960,796 - 28,102,441 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02328,016,442 - 28,158,900 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02328,271,892 - 28,414,438 (+)NCBIUU_Cfam_GSD_1.0
COL6A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383130,516,720 - 130,677,042 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3130,517,177 - 130,677,044 (+)EnsemblGRCh38hg38GRCh38
GRCh373130,236,021 - 130,395,886 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363131,761,868 - 131,878,578 (+)NCBINCBI36Build 36hg18NCBI36
Celera3128,706,262 - 128,821,161 (+)NCBICelera
Cytogenetic Map3q22.1NCBI
HuRef3127,663,926 - 127,780,510 (+)NCBIHuRef
CHM1_13130,242,015 - 130,358,892 (+)NCBICHM1_1
T2T-CHM13v2.03133,260,574 - 133,420,884 (+)NCBIT2T-CHM13v2.0
Col6a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399105,566,616 - 105,705,413 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9105,565,008 - 105,705,359 (-)EnsemblGRCm39 Ensembl
GRCm389105,689,417 - 105,828,246 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9105,687,809 - 105,828,160 (-)EnsemblGRCm38mm10GRCm38
MGSCv379105,591,747 - 105,730,415 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369105,632,212 - 105,667,748 (-)NCBIMGSCv36mm8
Celera9105,286,549 - 105,432,429 (-)NCBICelera
Cytogenetic Map9F1NCBI
cM Map956.99NCBI
Col6a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88115,196,833 - 115,352,161 (-)NCBIGRCr8
mRatBN7.28106,318,010 - 106,473,419 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8106,306,422 - 106,473,472 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.08114,352,130 - 114,449,993 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8114,353,825 - 114,449,956 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08113,727,475 - 113,872,124 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48110,793,849 - 110,892,578 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18110,810,892 - 110,935,930 (-)NCBI
Celera8105,644,636 - 105,799,150 (-)NCBICelera
Cytogenetic Map8q32NCBI
Col6a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555017,685,029 - 7,775,899 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555017,683,344 - 7,816,859 (-)NCBIChiLan1.0ChiLan1.0
LOC100968217
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22128,481,833 - 128,635,861 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13128,486,584 - 128,641,462 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03127,610,752 - 127,764,533 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13134,977,054 - 135,087,602 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3134,977,079 - 135,086,060 (+)Ensemblpanpan1.1panPan2
Col6a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560267,253,612 - 67,399,763 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365294,055,824 - 4,147,919 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365294,055,824 - 4,158,765 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL6A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl131,817,406 - 1,985,799 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1131,817,475 - 1,985,968 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2131,589,237 - 1,619,256 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL6A6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11559,517,463 - 59,671,767 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1559,519,231 - 59,670,639 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604132,546,006 - 32,654,340 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col6a6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247306,503,546 - 6,639,516 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247306,503,509 - 6,640,223 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in COL6A6
1904 total Variants

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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 1
Low 5 5 5 3 9 5
Below cutoff 5 17 6 6 6 1 6 12 5 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000009739   ⟹   ENSCAFP00000009041
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2327,759,103 - 27,900,154 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845049259   ⟹   ENSCAFP00845038658
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2328,265,670 - 28,407,244 (+)Ensembl
RefSeq Acc Id: XM_022408620   ⟹   XP_022264328
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12327,759,707 - 27,892,400 (+)NCBI
Dog10K_Boxer_Tasha2327,732,899 - 27,866,283 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038432279   ⟹   XP_038288207
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02328,265,751 - 28,407,486 (+)NCBI
RefSeq Acc Id: XM_038432280   ⟹   XP_038288208
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02328,265,749 - 28,399,268 (+)NCBI
RefSeq Acc Id: XM_038507577   ⟹   XP_038363505
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12327,960,796 - 28,102,441 (+)NCBI
RefSeq Acc Id: XM_038570819   ⟹   XP_038426747
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02328,271,894 - 28,414,438 (+)NCBI
RefSeq Acc Id: XM_038570820   ⟹   XP_038426748
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02328,271,892 - 28,404,656 (+)NCBI
RefSeq Acc Id: XM_038635013   ⟹   XP_038490941
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02328,016,442 - 28,158,900 (+)NCBI
RefSeq Acc Id: XM_848186   ⟹   XP_853279
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12327,759,708 - 27,900,971 (+)NCBI
Dog10K_Boxer_Tasha2327,732,901 - 27,874,490 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_853279   ⟸   XM_848186
- Peptide Label: isoform X2
- UniProtKB: A0A8P0N8J6 (UniProtKB/TrEMBL),   A0A8C0T547 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022264328   ⟸   XM_022408620
- Peptide Label: isoform X1
- UniProtKB: A0A8C0T547 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000009041   ⟸   ENSCAFT00000009739
RefSeq Acc Id: XP_038363505   ⟸   XM_038507577
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038490941   ⟸   XM_038635013
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038288208   ⟸   XM_038432280
- Peptide Label: isoform X1
- UniProtKB: A0A8C0PIB6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038288207   ⟸   XM_038432279
- Peptide Label: isoform X2
- UniProtKB: A0A8I3QF27 (UniProtKB/TrEMBL),   A0A8C0PIB6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038426748   ⟸   XM_038570820
- Peptide Label: isoform X1
- UniProtKB: A0A8C0T547 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038426747   ⟸   XM_038570819
- Peptide Label: isoform X2
- UniProtKB: A0A8C0T547 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845038658   ⟸   ENSCAFT00845049259
Protein Domains
VWFA


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000006035 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030025682 UniProtKB/TrEMBL
  ENSCAFG00040019167 UniProtKB/TrEMBL
  ENSCAFG00845027892 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000009739.5 UniProtKB/TrEMBL
  ENSCAFT00030047435.1 UniProtKB/TrEMBL
  ENSCAFT00040035479.1 UniProtKB/TrEMBL
  ENSCAFT00845049259 ENTREZGENE
  ENSCAFT00845049259.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
  6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene COL6A6 ENTREZGENE
PANTHER COLLAGEN ALPHA-6(VI) CHAIN UniProtKB/TrEMBL
  UNCHARACTERIZED UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
  VWA_3 UniProtKB/TrEMBL
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A8C0PIB6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0T547 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3QF27 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0N8J6 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:49850 ENTREZGENE