Col19a1 (collagen type XIX alpha 1 chain) - Rat Genome Database

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Gene: Col19a1 (collagen type XIX alpha 1 chain) Rattus norvegicus
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Symbol: Col19a1
Name: collagen type XIX alpha 1 chain
RGD ID: 1308920
Description: Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in cell adhesion; cell differentiation; and muscle organ development. Predicted to act upstream of or within extracellular matrix organization and skeletal muscle tissue development. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix. Orthologous to human COL19A1 (collagen type XIX alpha 1 chain); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: collagen alpha-1(XIX) chain; collagen, type XIX, alpha 1; LOC367236; procollagen, type XIX, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8934,170,248 - 34,518,478 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl934,170,248 - 34,518,350 (-)EnsemblGRCr8
mRatBN7.2926,673,916 - 27,022,139 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl926,675,391 - 27,022,106 (-)EnsemblmRatBN7.2
Rnor_6.0930,508,003 - 30,864,836 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl930,515,089 - 30,844,199 (-)Ensemblrn6Rnor6.0
Rnor_5.0929,332,121 - 29,688,495 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4923,003,618 - 23,337,800 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera924,210,032 - 24,556,238 (-)NCBICelera
RGSC_v3.1923,005,031 - 23,339,214 (-)NCBI
Cytogenetic Map9q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
8. The renaturation of procarboxypeptidase B by urea gradient gel filtration and some properties of recombinant carboxypeptidase B. Xiao-Yan Z, etal., Protein Pept Lett. 2005 Oct;12(7):671-6.
Additional References at PubMed
PMID:15302855  


Genomics

Comparative Map Data
Col19a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8934,170,248 - 34,518,478 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl934,170,248 - 34,518,350 (-)EnsemblGRCr8
mRatBN7.2926,673,916 - 27,022,139 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl926,675,391 - 27,022,106 (-)EnsemblmRatBN7.2
Rnor_6.0930,508,003 - 30,864,836 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl930,515,089 - 30,844,199 (-)Ensemblrn6Rnor6.0
Rnor_5.0929,332,121 - 29,688,495 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4923,003,618 - 23,337,800 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera924,210,032 - 24,556,238 (-)NCBICelera
RGSC_v3.1923,005,031 - 23,339,214 (-)NCBI
Cytogenetic Map9q21NCBI
COL19A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38669,866,556 - 70,212,468 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl669,866,556 - 70,212,468 (+)Ensemblhg38GRCh38
GRCh37670,576,448 - 70,922,171 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36670,633,169 - 70,978,878 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34670,633,168 - 70,978,881NCBI
Celera670,964,842 - 71,310,558 (+)NCBICelera
Cytogenetic Map6q13NCBI
HuRef667,767,231 - 67,800,831 (+)NCBIHuRef
HuRef667,828,725 - 68,120,497 (+)NCBIHuRef
CHM1_1670,742,652 - 71,088,489 (+)NCBICHM1_1
T2T-CHM13v2.0671,046,687 - 71,393,027 (+)NCBIT2T-CHM13v2.0
Col19a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,296,764 - 24,627,870 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl124,300,971 - 24,626,553 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38124,257,683 - 24,587,922 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl124,261,890 - 24,587,472 (-)Ensemblmm10GRCm38
MGSCv37124,264,522 - 24,594,276 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36124,218,269 - 24,541,686 (-)NCBIMGSCv36mm8
Celera124,095,365 - 24,420,936 (-)NCBICelera
Cytogenetic Map1A5NCBI
cM Map19.99NCBI
Col19a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554884,984,159 - 5,287,718 (+)Ensembl
ChiLan1.0NW_0049554884,984,140 - 5,288,530 (+)NCBIChiLan1.0ChiLan1.0
COL19A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2589,861,289 - 90,203,405 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1687,786,825 - 88,128,613 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0667,706,969 - 68,049,323 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1671,006,284 - 71,347,042 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl671,006,284 - 71,340,612 (+)EnsemblpanPan2panpan1.1
COL19A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11232,452,653 - 32,760,310 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1232,449,744 - 32,755,226 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1232,311,174 - 32,621,347 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01232,993,435 - 33,301,702 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1232,993,700 - 33,297,058 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11232,510,019 - 32,832,632 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01232,563,653 - 32,874,023 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01232,676,371 - 32,986,509 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Col19a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494667,699,359 - 68,012,743 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366181,868,564 - 2,165,131 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366181,856,473 - 2,169,869 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL19A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl150,045,065 - 50,399,969 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1150,044,394 - 50,402,256 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2156,204,150 - 56,562,463 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL19A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1174,769,466 - 5,096,036 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605810,782,130 - 11,117,453 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col19a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248199,673,233 - 9,996,628 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248199,668,052 - 10,023,511 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Col19a1
3223 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:102
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000017169
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
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)93125043268875676Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)92956766474567664Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)93125043265651574Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)92103143049025574Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)93145606157460683Rat


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
8 12 51 139 47 47 16 44 16 6 229 127 10 115 70 88 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000017169   ⟹   ENSRNOP00000017169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl934,170,248 - 34,518,350 (-)Ensembl
mRatBN7.2 Ensembl926,675,391 - 27,022,106 (-)Ensembl
Rnor_6.0 Ensembl930,515,089 - 30,844,199 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000130661   ⟹   ENSRNOP00000111686
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl934,170,248 - 34,518,350 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000147880   ⟹   ENSRNOP00000104672
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl934,170,248 - 34,518,350 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000149866   ⟹   ENSRNOP00000111345
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl934,170,248 - 34,518,038 (-)Ensembl
RefSeq Acc Id: NM_001421322   ⟹   NP_001408251
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8934,170,248 - 34,518,257 (-)NCBI
mRatBN7.2926,673,918 - 27,021,918 (-)NCBI
RefSeq Acc Id: XM_039084518   ⟹   XP_038940446
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8934,170,248 - 34,518,478 (-)NCBI
mRatBN7.2926,673,916 - 27,022,139 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001408251 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940446 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017169
  ENSRNOP00000017169.9
  ENSRNOP00000104672.1
  ENSRNOP00000111345.1
  ENSRNOP00000111686.1
Ensembl Acc Id: ENSRNOP00000017169   ⟸   ENSRNOT00000017169
RefSeq Acc Id: XP_038940446   ⟸   XM_039084518
- Peptide Label: isoform X1
- UniProtKB: D3ZCQ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001408251   ⟸   NM_001421322
- Peptide Label: precursor
- UniProtKB: D3ZCQ0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000104672   ⟸   ENSRNOT00000147880
Ensembl Acc Id: ENSRNOP00000111345   ⟸   ENSRNOT00000149866
Ensembl Acc Id: ENSRNOP00000111686   ⟸   ENSRNOT00000130661

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZCQ0-F1-model_v2 AlphaFold D3ZCQ0 1-1129 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:1308920 AgrOrtholog
BioCyc Gene G2FUF-27959 BioCyc
Ensembl Genes ENSRNOG00000012759 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017169 ENTREZGENE
  ENSRNOT00000017169.9 UniProtKB/TrEMBL
  ENSRNOT00000130661.1 UniProtKB/TrEMBL
  ENSRNOT00000147880.1 UniProtKB/TrEMBL
  ENSRNOT00000149866.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.200 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
  ConA-like_dom UniProtKB/TrEMBL
  TSPN-like_N UniProtKB/TrEMBL
NCBI Gene 367236 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN TRIPLE HELIX REPEAT UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
PhenoGen Col19a1 PhenoGen
RatGTEx ENSRNOG00000012759 RatGTEx
SMART TSPN UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt A0ABK0L4S2_RAT UniProtKB/TrEMBL
  A0ABK0LL36_RAT UniProtKB/TrEMBL
  A0ABK0LY07_RAT UniProtKB/TrEMBL
  D3ZCQ0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col19a1  collagen type XIX alpha 1 chain  Col19a1  collagen, type XIX, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-02-25 Col19a1  collagen, type XIX, alpha 1  Col19a1  procollagen, type XIX, alpha 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Col19a1  procollagen, type XIX, alpha 1   Col19a1_predicted  procollagen, type XIX, alpha 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Col19a1_predicted  procollagen, type XIX, alpha 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED