Col6a4 (collagen, type VI, alpha 4) - Rat Genome Database

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Gene: Col6a4 (collagen, type VI, alpha 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Col6a4
Name: collagen, type VI, alpha 4
RGD ID: 1564060
Description: Predicted to be involved in cell adhesion. Predicted to be located in extracellular region. Predicted to be part of collagen trimer; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Col6a4p1; collagen alpha-4(VI) chain; collagen, type VI, alpha 4 pseudogene 1; dual von Willebrand factor A domains; Dvwa; LOC315981; RGD1564060; similar to procollagen, type VI, alpha 3 isoform 4
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88115,495,886 - 115,612,229 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8115,495,886 - 115,611,841 (-)EnsemblGRCr8
mRatBN7.28106,617,169 - 106,733,493 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8106,617,050 - 106,733,263 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8112,246,080 - 112,341,379 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08110,445,250 - 110,540,553 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08108,288,057 - 108,383,359 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08114,670,628 - 114,766,803 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8114,670,631 - 114,766,803 (-)Ensemblrn6Rnor6.0
Rnor_5.08114,044,961 - 114,137,875 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.48111,013,085 - 111,138,091 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera8105,946,883 - 106,041,094 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Col6a4
831 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:109
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000047563
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
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
631217Activ1Activity QTL 115.9voluntary movement trait (VT:0003491)number of photobeam interruptions in an experimental apparatus (CMO:0001517)8111249511117802327Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
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
D8Got207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,679,470 - 106,679,674 (+)MAPPERmRatBN7.2
Rnor_6.08114,728,723 - 114,728,926NCBIRnor6.0
Rnor_5.08114,101,301 - 114,101,504UniSTSRnor5.0
RGSC_v3.48111,075,562 - 111,075,766RGDRGSC3.4
RGSC_v3.48111,075,563 - 111,075,766UniSTSRGSC3.4
Celera8106,003,597 - 106,003,800UniSTS
RGSC_v3.18111,095,018 - 111,095,221RGD
RH 3.4 Map81151.09UniSTS
RH 3.4 Map81151.09RGD
RH 2.0 Map8879.5RGD
Cytogenetic Map8q32UniSTS
AU024783  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.08114,102,077 - 114,102,171NCBIRnor5.0
RGSC_v3.48111,074,896 - 111,074,989UniSTSRGSC3.4
Cytogenetic Map8q32UniSTS
D11S3831  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28106,679,515 - 106,680,656 (+)MAPPERmRatBN7.2
Rnor_6.08114,728,768 - 114,729,908NCBIRnor6.0
Rnor_5.08114,101,346 - 114,102,486UniSTSRnor5.0
RGSC_v3.48111,074,580 - 111,075,721UniSTSRGSC3.4
Celera8106,003,642 - 106,004,783UniSTS
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
16 6 53 154 59 62 31 89 31 6 287 168 11 129 67 92 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000047563   ⟹   ENSRNOP00000042470
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8115,495,886 - 115,611,841 (-)Ensembl
mRatBN7.2 Ensembl8106,617,050 - 106,733,263 (-)Ensembl
Rnor_6.0 Ensembl8114,670,631 - 114,766,803 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111160   ⟹   ENSRNOP00000086989
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8115,495,886 - 115,611,841 (-)Ensembl
mRatBN7.2 Ensembl8106,617,050 - 106,733,263 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000123288   ⟹   ENSRNOP00000099719
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8115,495,886 - 115,611,841 (-)Ensembl
RefSeq Acc Id: NM_001412226   ⟹   NP_001399155
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88115,495,886 - 115,611,841 (-)NCBI
mRatBN7.28106,617,169 - 106,733,103 (-)NCBI
RefSeq Acc Id: XM_039081569   ⟹   XP_038937497
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88115,495,886 - 115,612,229 (-)NCBI
mRatBN7.28106,617,169 - 106,733,493 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001399155 (Get FASTA)   NCBI Sequence Viewer  
  XP_038937497 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77336 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000042470
  ENSRNOP00000042470.5
  ENSRNOP00000086989
  ENSRNOP00000086989.1
  ENSRNOP00000099719.1
Ensembl Acc Id: ENSRNOP00000042470   ⟸   ENSRNOT00000047563
RefSeq Acc Id: XP_038937497   ⟸   XM_039081569
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A6Y7 (UniProtKB/TrEMBL),   F1M6H4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000086989   ⟸   ENSRNOT00000111160
RefSeq Acc Id: NP_001399155   ⟸   NM_001412226
- Peptide Label: precursor
- UniProtKB: F1M6H4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000099719   ⟸   ENSRNOT00000123288
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M6H4-F1-model_v2 AlphaFold F1M6H4 1-2113 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:1564060 AgrOrtholog
BioCyc Gene G2FUF-29258 BioCyc
Ensembl Genes ENSRNOG00000031782 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047563 ENTREZGENE
  ENSRNOT00000047563.6 UniProtKB/TrEMBL
  ENSRNOT00000111160 ENTREZGENE
  ENSRNOT00000111160.2 UniProtKB/TrEMBL
  ENSRNOT00000123288.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  ECM_Assembly_Org UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 315981 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  VWFA DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
  VWA_3 UniProtKB/TrEMBL
PhenoGen Col6a4 PhenoGen
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031782 RatGTEx
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A8I6A6Y7 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L6W3_RAT UniProtKB/TrEMBL
  F1M6H4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-05 Col6a4  collagen, type VI, alpha 4  Col6a4p1  collagen, type VI, alpha 4 pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Col6a4p1  collagen, type VI, alpha 4 pseudogene 1  Dvwa  dual von Willebrand factor A domains  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-07 Dvwa  dual von Willebrand factor A domains  RGD1564060  similar to procollagen, type VI, alpha 3 isoform 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564060  similar to procollagen, type VI, alpha 3 isoform 4   RGD1564060_predicted  similar to procollagen, type VI, alpha 3 isoform 4 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 RGD1564060_predicted  similar to procollagen, type VI, alpha 3 isoform 4 (predicted)    similar to alpha-3 collagen type VI (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1564060_predicted  similar to alpha-3 collagen type VI (predicted)  LOC315981  similar to alpha-3 collagen type VI  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC315981  similar to alpha-3 collagen type VI      Symbol and Name status set to provisional 70820 PROVISIONAL