Col4a6 (collagen type IV alpha 6 chain) - Rat Genome Database

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Gene: Col4a6 (collagen type IV alpha 6 chain) Rattus norvegicus
Analyze
Symbol: Col4a6
Name: collagen type IV alpha 6 chain
RGD ID: 1589724
Description: Predicted to be an extracellular matrix structural constituent. Predicted to act upstream of or within cellular response to amino acid stimulus; collagen-activated tyrosine kinase receptor signaling pathway; and extracellular matrix organization. Predicted to be located in basement membrane. Predicted to be part of collagen type IV trimer. Human ortholog(s) of this gene implicated in X-linked deafness 6. Orthologous to human COL4A6 (collagen type IV alpha 6 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-6(IV) chain; collagen, type IV, alpha 6; LOC363458; similar to procollagen, type IV, alpha 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X104,766,463 - 105,117,499 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX104,766,957 - 105,117,500 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X112,405,647 - 112,768,337 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX112,405,647 - 112,473,822 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X110,869,083 - 111,225,229 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X37,316,545 - 37,485,511 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX104,184,917 - 104,528,021 (-)NCBICelera
Cytogenetic MapXq33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10534397   PMID:10965041   PMID:10970885   PMID:11732842   PMID:12101409   PMID:18757743   PMID:19275937   PMID:20548288  


Genomics

Comparative Map Data
Col4a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X104,766,463 - 105,117,499 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX104,766,957 - 105,117,500 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X112,405,647 - 112,768,337 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX112,405,647 - 112,473,822 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X110,869,083 - 111,225,229 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X37,316,545 - 37,485,511 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX104,184,917 - 104,528,021 (-)NCBICelera
Cytogenetic MapXq33NCBI
COL4A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X108,155,614 - 108,439,458 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX108,155,607 - 108,439,497 (-)EnsemblGRCh38hg38GRCh38
GRCh37X107,398,844 - 107,682,688 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X107,285,493 - 107,569,360 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X107,204,990 - 107,487,805NCBI
CeleraX107,870,304 - 108,154,135 (-)NCBICelera
Cytogenetic MapXq22.3NCBI
HuRefX97,021,267 - 97,304,612 (-)NCBIHuRef
CHM1_1X107,309,670 - 107,593,530 (-)NCBICHM1_1
T2T-CHM13v2.0X106,593,205 - 106,877,000 (-)NCBIT2T-CHM13v2.0
Col4a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X139,948,399 - 140,257,091 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX139,948,399 - 140,257,072 (-)EnsemblGRCm39 Ensembl
GRCm38X141,165,403 - 141,474,095 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX141,165,403 - 141,474,076 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X137,599,946 - 137,908,619 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X136,412,396 - 136,720,444 (-)NCBIMGSCv36mm8
CeleraX125,173,938 - 125,484,194 (-)NCBICelera
Cytogenetic MapXF1- F2NCBI
cM MapX61.8NCBI
Col4a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554907,409,160 - 7,762,929 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554907,409,687 - 7,764,300 (+)NCBIChiLan1.0ChiLan1.0
COL4A6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X107,641,123 - 107,924,392 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X97,254,306 - 97,539,473 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X107,612,289 - 107,909,373 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX107,625,718 - 107,908,363 (-)Ensemblpanpan1.1panPan2
COL4A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X81,690,047 - 81,981,005 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX81,691,417 - 81,980,703 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX67,810,622 - 68,101,637 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X83,339,380 - 83,630,482 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX83,339,378 - 83,630,109 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X80,798,389 - 81,089,594 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X82,510,974 - 82,802,154 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X82,301,801 - 82,589,247 (-)NCBIUU_Cfam_GSD_1.0
Col4a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X81,017,535 - 81,295,934 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364996,362,295 - 6,639,047 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364996,421,930 - 6,640,429 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX88,634,930 - 88,957,416 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X88,634,925 - 88,750,938 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X103,072,846 - 103,136,037 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL4A6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X96,012,442 - 96,307,911 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606521,110,813 - 21,404,844 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col4a6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248037,917,668 - 8,335,274 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Col4a6
1044 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:89
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000040428, ENSRNOT00000052169
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat

Markers in Region
AU047046  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X105,105,656 - 105,105,776 (+)MAPPERmRatBN7.2
Rnor_6.0X112,756,484 - 112,756,603NCBIRnor6.0
Rnor_5.0X111,213,392 - 111,213,511UniSTSRnor5.0
RGSC_v3.4X37,143,646 - 37,143,765UniSTSRGSC3.4
CeleraX104,516,168 - 104,516,287UniSTS
Cytogenetic MapXq14UniSTS
AU049795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X105,054,231 - 105,054,439 (+)MAPPERmRatBN7.2
mRatBN7.2X105,054,231 - 105,054,446 (+)MAPPERmRatBN7.2
Rnor_6.0X112,705,321 - 112,705,531NCBIRnor6.0
Rnor_6.0X112,705,321 - 112,705,524NCBIRnor6.0
Rnor_5.0X111,160,504 - 111,160,714UniSTSRnor5.0
Rnor_5.0X111,160,504 - 111,160,707UniSTSRnor5.0
RGSC_v3.4X37,196,153 - 37,196,363UniSTSRGSC3.4
CeleraX104,465,732 - 104,465,942UniSTS
CeleraX104,465,732 - 104,465,935UniSTS
Cytogenetic MapXq14UniSTS
RH132646  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X104,766,601 - 104,766,809 (+)MAPPERmRatBN7.2
Rnor_6.0X112,404,490 - 112,404,697NCBIRnor6.0
Rnor_5.0X110,866,447 - 110,866,654UniSTSRnor5.0
CeleraX104,185,925 - 104,186,132UniSTS
RH 3.4 Map71125.51UniSTS
Cytogenetic MapXq14UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium 10 2 2 2 16 2 20 10
Low 2 30 28 12 16 12 2 2 58 33 21 1 2
Below cutoff 1 3 21 21 3 21 6 9 6

Sequence


RefSeq Acc Id: ENSRNOT00000079180   ⟹   ENSRNOP00000073623
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX104,766,957 - 105,117,500 (-)Ensembl
Rnor_6.0 EnsemblX112,405,647 - 112,473,822 (-)Ensembl
RefSeq Acc Id: XM_039100524   ⟹   XP_038956452
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X104,766,463 - 105,117,499 (-)NCBI
RefSeq Acc Id: XM_039100525   ⟹   XP_038956453
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X104,769,933 - 105,117,499 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414189 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956452 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956453 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000073623
  ENSRNOP00000073623.2
RefSeq Acc Id: ENSRNOP00000073623   ⟸   ENSRNOT00000079180
RefSeq Acc Id: XP_038956452   ⟸   XM_039100524
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038956453   ⟸   XM_039100525
- Peptide Label: isoform X2
Protein Domains
Collagen IV NC1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K601-F1-model_v2 AlphaFold A0A0G2K601 1-1638 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:1589724 AgrOrtholog
BioCyc Gene G2FUF-1528 BioCyc
Ensembl Genes ENSRNOG00000056772 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079180 ENTREZGENE
  ENSRNOT00000079180.2 UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/TrEMBL
InterPro C-type_lectin_fold UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/TrEMBL
  Collagen_VI_NC UniProtKB/TrEMBL
NCBI Gene 363458 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-6(IV) CHAIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PhenoGen Col4a6 PhenoGen
PROSITE NC1_IV UniProtKB/TrEMBL
RatGTEx ENSRNOG00000056772 RatGTEx
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
UniProt A0A0G2K601 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col4a6  collagen type IV alpha 6 chain  Col4a6  collagen, type IV, alpha 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-09 Col4a6  collagen, type IV, alpha 6  LOC363458  similar to procollagen, type IV, alpha 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC363458  similar to procollagen, type IV, alpha 6      Symbol and Name status set to provisional 70820 PROVISIONAL