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 extracellular matrix. Human ortholog(s) of this gene implicated in Marshall syndrome; Stickler syndrome 2; autosomal dominant nonsyndromic deafness 37; 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82204,509,136 - 204,702,264 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)EnsemblGRCr8
mRatBN7.22201,820,715 - 202,013,853 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2201,820,715 - 202,013,853 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2209,434,815 - 209,630,095 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02207,330,639 - 207,525,948 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02202,147,647 - 202,342,953 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02216,863,423 - 217,056,523 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2216,863,428 - 217,056,523 (+)Ensemblrn6Rnor6.0
Rnor_5.02234,955,150 - 235,148,754 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42209,996,467 - 210,193,379 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2194,360,332 - 194,556,704 (+)NCBICelera
RGSC_v3.12210,124,200 - 210,156,132 (+)NCBI
Cytogenetic Map2q42NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (ISO)
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)
2,4,4'-trichlorobiphenyl  (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)
Azoxymethane  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (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)
okadaic acid  (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 arsenate  (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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)EnsemblGRCr8
mRatBN7.22201,820,715 - 202,013,853 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2201,820,715 - 202,013,853 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2209,434,815 - 209,630,095 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02207,330,639 - 207,525,948 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02202,147,647 - 202,342,953 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02216,863,423 - 217,056,523 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2216,863,428 - 217,056,523 (+)Ensemblrn6Rnor6.0
Rnor_5.02234,955,150 - 235,148,754 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42209,996,467 - 210,193,379 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2194,360,332 - 194,556,704 (+)NCBICelera
RGSC_v3.12210,124,200 - 210,156,132 (+)NCBI
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 (-)Ensemblhg38GRCh38
GRCh371103,342,029 - 103,574,078 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361103,114,611 - 103,346,640 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm383114,030,479 - 114,220,756 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3114,030,540 - 114,220,718 (+)Ensemblmm10GRCm38
MGSCv373113,733,458 - 113,923,244 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha650,216,773 - 50,413,293 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0647,763,689 - 47,960,683 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248575,817,472 - 6,176,421 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Col11a1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1345,375,548 - 45,565,416 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Col11a1
1478 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2163997722225110681Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2169358774214358774Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2149957381221199885Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845370229470703Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283465462229820014Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2138595962205135428Rat
1581576Pur7Proteinuria QTL 70.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)280396178220931218Rat
152025245Scl81Serum cholesterol level QTL 813.49blood cholesterol amount (VT:0000180)2124537199209621565Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2145807215220931416Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2191709311217961898Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278269809208420281Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2122597372215234002Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)280396178220931218Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2159440891205135267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2196140964251540988Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170652929215652929Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2159440891220931218Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2171994826205135428Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2188565047233565047Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2192287802229609668Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2184856304229856304Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2184856304229856304Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2144882354205135428Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2191709311217961898Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)267845182205135428Rat
1357991Ael2Aortic elastin QTL 24.20.000071aorta elastin amount (VT:0003905)aortic elastin2169227906214227906Rat
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)283400752223709938Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2192287802221089121Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)244537979205135428Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2184856304229856304Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2192287802237287802Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)2175931416220931416Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)280396034220931416Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278269809205135428Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2182024327227024327Rat
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)2159440760228950743Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2184482291229482291Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2202029709236904960Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2143746578205135428Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2114384617215381366Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2145306936212705578Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2113746222205135428Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2186850607231850607Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2192287802237287802Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2114384617215381366Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660223841096Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2117415288205135428Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2182635347227635347Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283465462225110681Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)247856345205135428Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2175008837220008837Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2184856304229856304Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2203664411248664411Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2165453811210453811Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2163253030208253030Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166372086229820014Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)276328396209350714Rat

Markers in Region
D2Rat54  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr82204,524,174 - 204,524,480 (+)Marker Load Pipeline
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
Celera2194,375,288 - 194,375,593UniSTS
RGSC_v3.12209,974,716 - 209,975,021RGD
RH 3.4 Map21446.21UniSTS
RH 3.4 Map21446.21RGD
RH 2.0 Map1497.6RGD
SHRSP x BN Map278.4998RGD
FHH x ACI Map289.8599RGD
Cytogenetic Map2q41UniSTS
RH134389  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr82204,700,553 - 204,700,757 (+)Marker Load Pipeline
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
GRCr82204,509,258 - 204,509,415 (+)Marker Load Pipeline
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

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
10 12 65 159 86 85 54 86 54 6 337 184 11 138 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000068413   ⟹   ENSRNOP00000061595
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)Ensembl
mRatBN7.2 Ensembl2201,820,715 - 202,013,853 (+)Ensembl
Rnor_6.0 Ensembl2216,863,428 - 217,056,523 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000144283   ⟹   ENSRNOP00000109210
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000152644   ⟹   ENSRNOP00000110050
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000160024   ⟹   ENSRNOP00000103446
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000164805   ⟹   ENSRNOP00000104130
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2204,509,136 - 204,702,264 (+)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
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:
Ensembl Acc Id: ENSRNOP00000061595   ⟸   ENSRNOT00000068413
RefSeq Acc Id: XP_063137444   ⟸   XM_063281374
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000103446   ⟸   ENSRNOT00000160024
Ensembl Acc Id: ENSRNOP00000104130   ⟸   ENSRNOT00000164805
Ensembl Acc Id: ENSRNOP00000110050   ⟸   ENSRNOT00000152644
Ensembl Acc Id: ENSRNOP00000109210   ⟸   ENSRNOT00000144283
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
Ensembl Transcript ENSRNOT00000068413 ENTREZGENE
  ENSRNOT00000068413.4 UniProtKB/Swiss-Prot
  ENSRNOT00000144283 ENTREZGENE
Gene3D-CATH 2.60.120.1000 UniProtKB/Swiss-Prot
  2.60.120.200 UniProtKB/Swiss-Prot
InterPro Collagen UniProtKB/Swiss-Prot
  Collagen_superfamily UniProtKB/Swiss-Prot
  ConA-like_dom_sf UniProtKB/Swiss-Prot
  Fib_collagen_C UniProtKB/Swiss-Prot
  Laminin_G UniProtKB/Swiss-Prot
  TSPN-like_N UniProtKB/Swiss-Prot
KEGG Report rno:25654 UniProtKB/Swiss-Prot
NCBI Gene 25654 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/Swiss-Prot
  COLLAGEN TRIPLE HELIX REPEAT UniProtKB/Swiss-Prot
Pfam COLFI UniProtKB/Swiss-Prot
  Collagen UniProtKB/Swiss-Prot
  Laminin_G_2 UniProtKB/Swiss-Prot
PhenoGen Col11a1 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000023148 RatGTEx
SMART COLFI UniProtKB/Swiss-Prot
  LamG UniProtKB/Swiss-Prot
  TSPN UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot
TIGR TC228927
UniProt A0ABK0LH21_RAT UniProtKB/TrEMBL
  A0ABK0LKF3_RAT UniProtKB/TrEMBL
  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