Col6a6 (collagen type VI alpha 6 chain) - Rat Genome Database

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Gene: Col6a6 (collagen type VI alpha 6 chain) Rattus norvegicus
Analyze
Symbol: Col6a6
Name: collagen type VI alpha 6 chain
RGD ID: 1309172
Description: Predicted to be involved in extracellular matrix organization. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix. Orthologous to human COL6A6 (collagen type VI alpha 6 chain); PARTICIPATES IN cell-extracellular matrix signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-6(VI) chain; collagen, type VI, alpha 6; LOC315979; RGD1309172; similar to matrilin 3b; similar to RIKEN cDNA E330026B02
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88115,196,833 - 115,352,161 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8115,197,464 - 115,352,136 (-)EnsemblGRCr8
mRatBN7.28106,318,010 - 106,473,419 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8106,306,422 - 106,473,472 (-)EnsemblmRatBN7.2
Rnor_6.08114,352,130 - 114,449,993 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8114,353,825 - 114,449,956 (-)Ensemblrn6Rnor6.0
Rnor_5.08113,727,475 - 113,872,124 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48110,793,849 - 110,892,578 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8105,644,636 - 105,799,150 (-)NCBICelera
RGSC_v3.18110,810,892 - 110,935,930 (-)NCBI
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18400749   PMID:24563484   PMID:27559042  


Genomics

Comparative Map Data
Col6a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88115,196,833 - 115,352,161 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8115,197,464 - 115,352,136 (-)EnsemblGRCr8
mRatBN7.28106,318,010 - 106,473,419 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8106,306,422 - 106,473,472 (-)EnsemblmRatBN7.2
Rnor_6.08114,352,130 - 114,449,993 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8114,353,825 - 114,449,956 (-)Ensemblrn6Rnor6.0
Rnor_5.08113,727,475 - 113,872,124 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48110,793,849 - 110,892,578 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8105,644,636 - 105,799,150 (-)NCBICelera
RGSC_v3.18110,810,892 - 110,935,930 (-)NCBI
Cytogenetic Map8q32NCBI
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 (+)Ensemblhg38GRCh38
GRCh373130,236,021 - 130,395,886 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363131,761,868 - 131,878,578 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm389105,689,417 - 105,828,246 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9105,687,809 - 105,828,160 (-)Ensemblmm10GRCm38
MGSCv379105,591,747 - 105,730,415 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369105,632,212 - 105,667,748 (-)NCBIMGSCv36mm8
Celera9105,286,549 - 105,432,429 (-)NCBICelera
Cytogenetic Map9F1NCBI
cM Map956.99NCBI
Col6a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555017,685,029 - 7,775,899 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2327,732,899 - 27,874,490 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02328,265,749 - 28,407,486 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_Cfam_GSD_1.0
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 (+)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247306,503,509 - 6,640,223 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Col6a6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1896,982,242 - 97,079,065 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Col6a6
1654 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:41
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000056414
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)882352698127352698Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)861019838121662124Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)849849908118871671Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)880768445125768445Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)880768445125768445Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)870041301121080908Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)868690349119799881Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)884192326129192326Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
8693654Alc32Alcohol consumption QTL 3220.755drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)897492344116428905Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)855428333127966348Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8111249511117802327Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)898145073122898010Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)880768445125768445Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)880768445125768445Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat

Markers in Region
RH132348  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,318,292 - 106,318,472 (+)MAPPERmRatBN7.2
Rnor_6.08114,352,394 - 114,352,573NCBIRnor6.0
Rnor_5.08113,727,676 - 113,727,855UniSTSRnor5.0
RGSC_v3.48110,792,418 - 110,792,597UniSTSRGSC3.4
Celera8105,644,900 - 105,645,079UniSTS
RH 3.4 Map81150.6UniSTS
Cytogenetic Map8q32UniSTS
RH141195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,316,358 - 106,316,569 (+)MAPPERmRatBN7.2
Rnor_6.08114,350,460 - 114,350,670NCBIRnor6.0
Rnor_5.08113,725,742 - 113,725,952UniSTSRnor5.0
RGSC_v3.48110,790,484 - 110,790,694UniSTSRGSC3.4
Celera8105,642,966 - 105,643,176UniSTS
RH 3.4 Map81151.0UniSTS
Cytogenetic Map8q32UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
12 12 66 151 91 90 59 65 59 6 324 164 10 130 81 92 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000056414   ⟹   ENSRNOP00000053252
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8115,197,464 - 115,352,136 (-)Ensembl
mRatBN7.2 Ensembl8106,306,422 - 106,473,472 (-)Ensembl
Rnor_6.0 Ensembl8114,353,825 - 114,449,956 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098400   ⟹   ENSRNOP00000096819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8115,197,464 - 115,352,136 (-)Ensembl
mRatBN7.2 Ensembl8106,306,422 - 106,473,285 (-)Ensembl
RefSeq Acc Id: XM_039082609   ⟹   XP_038938537
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88115,196,833 - 115,333,286 (-)NCBI
mRatBN7.28106,318,010 - 106,454,599 (-)NCBI
RefSeq Acc Id: XM_039082610   ⟹   XP_038938538
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88115,218,497 - 115,352,161 (-)NCBI
mRatBN7.28106,329,339 - 106,473,419 (-)NCBI
RefSeq Acc Id: XM_063266454   ⟹   XP_063122524
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88115,218,497 - 115,352,161 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038938537 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938538 (Get FASTA)   NCBI Sequence Viewer  
  XP_063122524 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000053252
  ENSRNOP00000053252.5
  ENSRNOP00000096819.1
Ensembl Acc Id: ENSRNOP00000053252   ⟸   ENSRNOT00000056414
RefSeq Acc Id: XP_038938537   ⟸   XM_039082609
- Peptide Label: isoform X3
- UniProtKB: D3ZL10 (UniProtKB/TrEMBL),   A0A8I6GLS2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038938538   ⟸   XM_039082610
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000096819   ⟸   ENSRNOT00000098400
RefSeq Acc Id: XP_063122524   ⟸   XM_063266454
- Peptide Label: isoform X1
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZL10-F1-model_v2 AlphaFold D3ZL10 1-2264 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309172 AgrOrtholog
BioCyc Gene G2FUF-29267 BioCyc
Ensembl Genes ENSRNOG00000023007 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056414 ENTREZGENE
  ENSRNOT00000056414.6 UniProtKB/TrEMBL
  ENSRNOT00000098400.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
  6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  ECM_Assembly_Org UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 315979 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
  VWA_3 UniProtKB/TrEMBL
PhenoGen Col6a6 PhenoGen
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023007 RatGTEx
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A8I6GLS2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZL10 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col6a6  collagen type VI alpha 6 chain  Col6a6  collagen, type VI, alpha 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Col6a6  collagen, type VI, alpha 6  LOC686258  similar to matrilin 3b  Data merged from RGD:1584306 1643240 APPROVED
2010-02-12 Col6a6  collagen, type VI, alpha 6  RGD1309172  similar to RIKEN cDNA E330026B02   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309172  similar to RIKEN cDNA E330026B02   RGD1309172_predicted  similar to RIKEN cDNA E330026B02 (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 RGD1309172_predicted  similar to RIKEN cDNA E330026B02 (predicted)  LOC686266  similar to alpha 3 type VI collagen isoform 1 precursor  Data merged from RGD:1584298 1643240 APPROVED
2006-11-19 LOC686266  similar to alpha 3 type VI collagen isoform 1 precursor      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC686258  similar to matrilin 3b      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1309172_predicted  similar to RIKEN cDNA E330026B02 (predicted)  LOC315979_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC315979_predicted  similar to RIKEN cDNA E330026B02 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL