Col11a1 (collagen type XI alpha 1 chain) - Rat Genome Database

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Gene: Col11a1 (collagen type XI alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col11a1
Name: collagen type XI alpha 1 chain
RGD ID: 2372
Description: Enables heparan sulfate binding activity and heparin binding activity. Involved in ossification. Located in collagen-containing extracellular matrix. Human ortholog(s) of this gene implicated in Marshall syndrome; Stickler syndrome 2; autosomal dominant nonsyndromic deafness; and fibrochondrogenesis 1. Orthologous to human COL11A1 (collagen type XI alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-1(XI) chain; collagen type a1(XI)6A-7-8; collagen type a1(XI)6B-7; collagen type XI; collagen, type XI, alpha 1; Procollagen type XI alpha 1; Procollagen type XI alpha 1,; procollagen, type XI, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82204,509,136 - 204,702,264 (+)NCBIGRCr8
mRatBN7.22201,820,715 - 202,013,853 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2201,820,715 - 202,013,853 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2209,434,815 - 209,630,095 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02207,330,639 - 207,525,948 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02202,147,647 - 202,342,953 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02216,863,423 - 217,056,523 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2216,863,428 - 217,056,523 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02234,955,150 - 235,148,754 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42209,996,467 - 210,193,379 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12210,124,200 - 210,156,132 (+)NCBI
Celera2194,360,332 - 194,556,704 (+)NCBICelera
Cytogenetic Map2q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetohydrazide  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alachlor  (EXP)
aldehydo-D-glucosamine  (EXP)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
aluminium oxide  (ISO)
amiodarone  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon monoxide  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
ciglitazone  (EXP)
cisplatin  (ISO)
clobetasol  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
DDT  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diethyl malate  (ISO)
dimethyl sulfoxide  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (EXP,ISO)
fenamidone  (ISO)
furan  (EXP)
genistein  (EXP)
glycidol  (EXP)
hydrazine  (ISO)
ibuprofen  (ISO)
ketamine  (EXP)
lead diacetate  (EXP)
mercaptopurine  (EXP)
mercury dibromide  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
mitoxantrone  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
oxaliplatin  (EXP)
panobinostat  (ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
Ptaquiloside  (ISO)
purine-6-thiol  (EXP)
raloxifene  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium dodecyl sulfate  (ISO)
sulfur dioxide  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
Trapidil  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Marshall syndrome associated with a splicing defect at the COL11A1 locus. Griffith AJ, etal., Am J Hum Genet. 1998 Apr;62(4):816-23.
4. BMP-1-mediated proteolytic processing of alternatively spliced isoforms of collagen type XI. Medeck RJ, etal., Biochem J 2003 Dec 1;376(Pt 2):361-8.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. Alternative exon splicing within the amino-terminal nontriple-helical domain of the rat pro-alpha 1(XI) collagen chain generates multiple forms of the mRNA transcript which exhibit tissue-dependent variation. Oxford JT, etal., J Biol Chem 1995 Apr 21;270(16):9478-85.
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
15. Isoform-specific heparan sulfate binding within the amino-terminal noncollagenous domain of collagen alpha1(XI). Warner LR, etal., J Biol Chem. 2006 Dec 22;281(51):39507-16. Epub 2006 Oct 24.
16. Collagen mRNA expression during tissue development: the temporospacial order coordinates bone morphogenesis with collagen fiber formation. Wurtz T, etal., Matrix Biol 1998 Oct;17(5):349-60.
Additional References at PubMed
PMID:886247   PMID:1952599   PMID:3070812   PMID:3182841   PMID:4100752   PMID:4110409   PMID:7859283   PMID:8872475   PMID:10573014   PMID:10889003   PMID:11731275   PMID:17029294  
PMID:17683922   PMID:21467034   PMID:22206666   PMID:23154389   PMID:24006456   PMID:24735995   PMID:29577904  


Genomics

Comparative Map Data
Col11a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82204,509,136 - 204,702,264 (+)NCBIGRCr8
mRatBN7.22201,820,715 - 202,013,853 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2201,820,715 - 202,013,853 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2209,434,815 - 209,630,095 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02207,330,639 - 207,525,948 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02202,147,647 - 202,342,953 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02216,863,423 - 217,056,523 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2216,863,428 - 217,056,523 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02234,955,150 - 235,148,754 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42209,996,467 - 210,193,379 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12210,124,200 - 210,156,132 (+)NCBI
Celera2194,360,332 - 194,556,704 (+)NCBICelera
Cytogenetic Map2q42NCBI
COL11A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381102,876,473 - 103,108,522 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1102,876,467 - 103,108,872 (-)EnsemblGRCh38hg38GRCh38
GRCh371103,342,029 - 103,574,078 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361103,114,611 - 103,346,640 (-)NCBINCBI36Build 36hg18NCBI36
Build 341103,055,015 - 103,286,073NCBI
Celera1101,611,302 - 101,843,503 (-)NCBICelera
Cytogenetic Map1p21.1NCBI
HuRef1101,474,202 - 101,706,091 (-)NCBIHuRef
CHM1_11103,456,836 - 103,688,896 (-)NCBICHM1_1
T2T-CHM13v2.01102,725,394 - 102,957,399 (-)NCBIT2T-CHM13v2.0
Col11a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393113,823,933 - 114,014,405 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3113,824,189 - 114,014,367 (+)EnsemblGRCm39 Ensembl
GRCm383114,030,479 - 114,220,756 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3114,030,540 - 114,220,718 (+)EnsemblGRCm38mm10GRCm38
MGSCv373113,733,458 - 113,923,244 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363114,022,729 - 114,212,291 (+)NCBIMGSCv36mm8
Celera3120,412,886 - 120,608,803 (+)NCBICelera
Cytogenetic Map3F3NCBI
cM Map349.35NCBI
Col11a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554357,352,617 - 7,545,235 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554357,352,617 - 7,545,235 (-)NCBIChiLan1.0ChiLan1.0
COL11A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21123,914,833 - 124,148,532 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11123,073,144 - 123,305,897 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01105,538,215 - 105,769,973 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11104,248,931 - 104,481,259 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1104,249,891 - 104,481,259 (-)Ensemblpanpan1.1panPan2
COL11A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1647,425,387 - 47,622,189 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl647,425,307 - 47,621,012 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha650,216,773 - 50,413,293 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0647,763,689 - 47,960,683 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl647,763,328 - 47,960,644 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1647,451,643 - 47,648,400 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0647,426,299 - 47,623,012 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0647,863,598 - 48,060,623 (+)NCBIUU_Cfam_GSD_1.0
Col11a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058112,882,302 - 113,096,413 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936730468,039 - 680,753 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936730466,912 - 680,823 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL11A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4115,634,172 - 115,840,708 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14115,638,381 - 115,841,679 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24127,267,387 - 127,409,238 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL11A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12030,284,471 - 30,508,660 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2030,284,447 - 30,508,658 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603827,625,255 - 27,850,627 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col11a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248575,817,475 - 6,029,107 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248575,817,472 - 6,176,421 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Col11a1
1775 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1154
Count of miRNA genes:268
Interacting mature miRNAs:336
Transcripts:ENSRNOT00000023693, ENSRNOT00000023794, ENSRNOT00000024138, ENSRNOT00000068413
Prediction methods:Microtar, Miranda, 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
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2184114274202447032Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2189599258218414891Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2189599258226936289Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2190613715226808892Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2199341726234244620Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat

Markers in Region
D2Rat54  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22201,835,753 - 201,836,059 (+)MAPPERmRatBN7.2
Rnor_6.02216,878,470 - 216,878,775NCBIRnor6.0
Rnor_5.02234,970,021 - 234,970,326UniSTSRnor5.0
RGSC_v3.42210,011,962 - 210,012,267UniSTSRGSC3.4
RGSC_v3.42210,011,961 - 210,012,267RGDRGSC3.4
RGSC_v3.12209,974,716 - 209,975,021RGD
Celera2194,375,288 - 194,375,593UniSTS
RH 3.4 Map21446.21RGD
RH 3.4 Map21446.21UniSTS
RH 2.0 Map1497.6RGD
SHRSP x BN Map278.4998RGD
FHH x ACI Map289.8599RGD
Cytogenetic Map2q41UniSTS
RH134389  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22202,012,142 - 202,012,346 (+)MAPPERmRatBN7.2
Rnor_6.02217,054,813 - 217,055,016NCBIRnor6.0
Rnor_5.02235,147,044 - 235,147,247UniSTSRnor5.0
RGSC_v3.42210,192,090 - 210,192,293UniSTSRGSC3.4
Celera2194,554,994 - 194,555,197UniSTS
RH 3.4 Map21451.0UniSTS
Cytogenetic Map2q41UniSTS
AI599979  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22202,013,242 - 202,013,393 (+)MAPPERmRatBN7.2
Rnor_6.02217,055,913 - 217,056,063NCBIRnor6.0
Rnor_5.02235,148,144 - 235,148,294UniSTSRnor5.0
RGSC_v3.42210,193,190 - 210,193,340UniSTSRGSC3.4
Celera2194,556,094 - 194,556,244UniSTS
RH 3.4 Map21452.8UniSTS
Cytogenetic Map2q41UniSTS
AI230651  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22201,820,837 - 201,820,994 (+)MAPPERmRatBN7.2
Rnor_6.02216,863,551 - 216,863,707NCBIRnor6.0
Rnor_5.02234,955,277 - 234,955,433UniSTSRnor5.0
RGSC_v3.42209,996,590 - 209,996,746UniSTSRGSC3.4
Celera2194,360,455 - 194,360,611UniSTS
RH 3.4 Map21446.2UniSTS
Cytogenetic Map2q41UniSTS


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 2 4 4 4 60 18 27 4
Low 26 30 14 15 14 3 6 14 17 10 8 3
Below cutoff 2 13 25 25 25 1 1 4 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068413   ⟹   ENSRNOP00000061595
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2201,820,715 - 202,013,853 (+)Ensembl
Rnor_6.0 Ensembl2216,863,428 - 217,056,523 (+)Ensembl
RefSeq Acc Id: NM_013117   ⟹   NP_037249
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82204,509,136 - 204,702,264 (+)NCBI
mRatBN7.22201,820,715 - 202,013,853 (+)NCBI
Rnor_6.02216,863,428 - 217,056,523 (+)NCBI
Rnor_5.02234,955,150 - 235,148,754 (+)NCBI
Celera2194,360,332 - 194,556,704 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233210   ⟹   XP_006233272
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82204,509,142 - 204,701,837 (+)NCBI
mRatBN7.22201,820,719 - 202,013,432 (+)NCBI
Rnor_6.02216,863,423 - 217,056,102 (+)NCBI
Rnor_5.02234,955,150 - 235,148,754 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063281374   ⟹   XP_063137444
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82204,602,970 - 204,701,837 (+)NCBI
RefSeq Acc Id: XR_010063586
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82204,509,141 - 204,634,310 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_037249   ⟸   NM_013117
- Peptide Label: precursor
- UniProtKB: Q921A0 (UniProtKB/Swiss-Prot),   Q920Z9 (UniProtKB/Swiss-Prot),   Q920Z8 (UniProtKB/Swiss-Prot),   Q920Z7 (UniProtKB/Swiss-Prot),   Q8VBY8 (UniProtKB/Swiss-Prot),   Q63393 (UniProtKB/Swiss-Prot),   Q63392 (UniProtKB/Swiss-Prot),   Q63391 (UniProtKB/Swiss-Prot),   Q62750 (UniProtKB/Swiss-Prot),   F1LSI4 (UniProtKB/Swiss-Prot),   Q921A1 (UniProtKB/Swiss-Prot),   P20909 (UniProtKB/Swiss-Prot),   A6HV70 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233272   ⟸   XM_006233210
- Peptide Label: isoform X2
- UniProtKB: A6HV70 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061595   ⟸   ENSRNOT00000068413
RefSeq Acc Id: XP_063137444   ⟸   XM_063281374
- Peptide Label: isoform X1
Protein Domains
Collagen-like   Fibrillar collagen NC1   Laminin G   Laminin G-like   Thrombospondin-like N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P20909-F1-model_v2 AlphaFold P20909 1-1804 view protein structure

Transcriptome

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

Promoters
RGD ID:13691696
Promoter ID:EPDNEW_R2221
Type:initiation region
Name:Col11a1_1
Description:collagen type XI alpha 1 chain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02216,863,520 - 216,863,580EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2372 AgrOrtholog
BioCyc Gene G2FUF-51531 BioCyc
Ensembl Genes ENSRNOG00000023148 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055001042 UniProtKB/Swiss-Prot
  ENSRNOG00060000945 UniProtKB/Swiss-Prot
  ENSRNOG00065022693 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000068413 ENTREZGENE
  ENSRNOT00000068413.4 UniProtKB/Swiss-Prot
  ENSRNOT00055001737 UniProtKB/Swiss-Prot
  ENSRNOT00060001250 UniProtKB/Swiss-Prot
  ENSRNOT00065038774 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSPN-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25654 UniProtKB/Swiss-Prot
NCBI Gene 25654 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(IV) CHAIN UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XI) CHAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MULTIPLEXIN, ISOFORM R UniProtKB/TrEMBL
  ZGC:113232 UniProtKB/TrEMBL
Pfam COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Col11a1 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023148 RatGTEx
  ENSRNOG00055001042 RatGTEx
  ENSRNOG00060000945 RatGTEx
  ENSRNOG00065022693 RatGTEx
SMART COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LamG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSPN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Concanavalin A-like lectins/glucanases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
TIGR TC228927
UniProt A6HV68_RAT UniProtKB/TrEMBL
  A6HV69_RAT UniProtKB/TrEMBL
  A6HV70 ENTREZGENE, UniProtKB/TrEMBL
  A6HV71_RAT UniProtKB/TrEMBL
  COBA1_RAT UniProtKB/Swiss-Prot
  F1LSI4 ENTREZGENE
  P20909 ENTREZGENE
  Q62750 ENTREZGENE
  Q63391 ENTREZGENE
  Q63392 ENTREZGENE
  Q63393 ENTREZGENE
  Q8VBY8 ENTREZGENE
  Q920Z7 ENTREZGENE
  Q920Z8 ENTREZGENE
  Q920Z9 ENTREZGENE
  Q921A0 ENTREZGENE
  Q921A1 ENTREZGENE
UniProt Secondary F1LSI4 UniProtKB/Swiss-Prot
  Q62750 UniProtKB/Swiss-Prot
  Q63391 UniProtKB/Swiss-Prot
  Q63392 UniProtKB/Swiss-Prot
  Q63393 UniProtKB/Swiss-Prot
  Q8VBY8 UniProtKB/Swiss-Prot
  Q920Z7 UniProtKB/Swiss-Prot
  Q920Z8 UniProtKB/Swiss-Prot
  Q920Z9 UniProtKB/Swiss-Prot
  Q921A0 UniProtKB/Swiss-Prot
  Q921A1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col11a1  collagen type XI alpha 1 chain  Col11a1  collagen, type XI, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Col11a1  collagen, type XI, alpha 1  Col11a1  procollagen, type XI, alpha 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Col11a1  procollagen, type XI, alpha 1     Procollagen type XI alpha 1,  Name updated 625702 APPROVED
2002-06-10 Col11a1  Procollagen type XI alpha 1,      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in nasal chondroblasts and transiently expressed in differentiating osteoblasts during embryonic development 70694
gene_function integral component of cartilage collagen fibrils 1300045
gene_function subunit of heterotrimeric collagen XI molecule 1300046
gene_physical_interaction may serve as a substrate for BMP-1 1300046
gene_process plays a role in regulation of collagen fibril diameter size 1300046
gene_transcript differential exon usage generates different transcripts depending on whether the gene is expressed in cartilage or non-cartilage tissues 1300045
gene_transcript expressed as six possible isoforms due to alternative splicing 1300046