Col11a2 (collagen type XI alpha 2 chain) - Rat Genome Database

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Gene: Col11a2 (collagen type XI alpha 2 chain) Rattus norvegicus
Analyze
Symbol: Col11a2
Name: collagen type XI alpha 2 chain
RGD ID: 2373
Description: Predicted to be an extracellular matrix structural constituent. Involved in osteoblast differentiation. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in cleft palate; nonsyndromic deafness (multiple); and osteochondrodysplasia (multiple). Orthologous to human COL11A2 (collagen type XI alpha 2 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Col11a2_mapped; collagen alpha-2(XI) chain; collagen alpha-2(XI) chain-like; collagen, type XI, alpha 2; LOC100911886; procollagen, type XI, alpha 2; procollagen, type XI, alpha 2 (mapped); type XI collagen alpha2 chain
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
mRatBN7.2204,786,929 - 4,816,598 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
Rnor_6.0203,829,324 - 3,859,022 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,830,164 - 3,859,018 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,908,541 - 5,938,415 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,924,452 - 4,953,310 (-)NCBIRGSC3.4rn4RGSC3.4
Celera206,387,407 - 6,415,975 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8662089   PMID:9188673   PMID:10581026   PMID:11237662   PMID:11668593   PMID:12673280   PMID:16033917   PMID:17683922  


Genomics

Comparative Map Data
Col11a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,786,929 - 4,816,598 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
Rnor_6.0203,829,324 - 3,859,022 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,830,164 - 3,859,018 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,908,541 - 5,938,415 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,924,452 - 4,953,310 (-)NCBIRGSC3.4rn4RGSC3.4
Celera206,387,407 - 6,415,975 (-)NCBICelera
Cytogenetic Map20p12NCBI
COL11A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl633,162,681 - 33,192,499 (-)EnsemblGRCh38hg38GRCh38
GRCh38633,162,692 - 33,193,009 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37633,130,471 - 33,160,244 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,238,447 - 33,268,223 (-)NCBINCBI36hg18NCBI36
Build 34633,238,446 - 33,268,223NCBI
Celera634,684,835 - 34,714,611 (-)NCBI
Cytogenetic Map6p21.32NCBI
HuRef632,872,882 - 32,902,658 (-)NCBIHuRef
CHM1_1633,132,343 - 33,162,118 (-)NCBICHM1_1
Col11a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,257,462 - 34,285,659 (+)NCBIGRCm39mm39
GRCm39 Ensembl1734,258,411 - 34,285,659 (+)Ensembl
GRCm381734,038,919 - 34,066,684 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,039,437 - 34,066,685 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,176,382 - 34,203,187 (+)NCBIGRCm37mm9NCBIm37
MGSCv361733,649,891 - 33,676,696 (+)NCBImm8
Celera1736,785,570 - 36,812,404 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
Col11a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,740,402 - 1,766,490 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,739,426 - 1,767,087 (-)NCBIChiLan1.0ChiLan1.0
COL11A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1633,849,885 - 33,879,635 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,849,885 - 33,879,635 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0632,734,950 - 32,765,837 (-)NCBIMhudiblu_PPA_v0panPan3
COL11A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,626,829 - 2,656,680 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,627,828 - 2,655,814 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,707,991 - 2,737,297 (-)NCBI
ROS_Cfam_1.0122,957,578 - 2,986,887 (-)NCBI
ROS_Cfam_1.0 Ensembl122,958,209 - 2,986,569 (-)Ensembl
UMICH_Zoey_3.1122,625,789 - 2,654,790 (-)NCBI
UNSW_CanFamBas_1.0122,707,183 - 2,736,164 (-)NCBI
UU_Cfam_GSD_1.0122,781,723 - 2,811,021 (-)NCBI
Col11a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,267,952 - 38,297,103 (-)NCBI
SpeTri2.0NW_00493647625,663,563 - 25,692,315 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL11A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl725,204,496 - 25,234,888 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1725,204,496 - 25,234,880 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2729,768,749 - 29,799,129 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL11A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,882,591 - 38,912,602 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1738,882,745 - 38,911,625 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604432,996,813 - 33,026,801 (-)NCBIVero_WHO_p1.0
Col11a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475423,614,486 - 23,640,489 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D20Yum79  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,795,650 - 4,795,808 (-)MAPPERmRatBN7.2
Rnor_6.0203,850,143 - 3,850,300NCBIRnor6.0
Rnor_5.0205,929,536 - 5,929,693UniSTSRnor5.0
RGSC_v3.4204,933,174 - 4,933,331UniSTSRGSC3.4
Celera206,396,129 - 6,396,284UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:237626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,816,872 - 4,817,110 (-)MAPPERmRatBN7.2
Rnor_6.0203,828,843 - 3,829,080NCBIRnor6.0
Rnor_5.0205,908,174 - 5,908,411UniSTSRnor5.0
RGSC_v3.4204,954,394 - 4,954,631UniSTSRGSC3.4
Celera206,417,059 - 6,417,296UniSTS
Cytogenetic Map20p12UniSTS
UniSTS:463405  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,787,570 - 4,788,444 (-)MAPPERmRatBN7.2
Rnor_6.0203,857,507 - 3,858,380NCBIRnor6.0
Rnor_5.0205,936,900 - 5,937,773UniSTSRnor5.0
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2047270785024580Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:230
Count of miRNA genes:148
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000045533
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.


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 4 5 23 4
Low 3 41 18 2 19 2 3 5 51 35 40 11 3
Below cutoff 2 39 39 39 1 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_212528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255929 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772720 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601583 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC098547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X95873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000045533   ⟹   ENSRNOP00000048846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
Rnor_6.0 Ensembl203,830,164 - 3,859,018 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084117   ⟹   ENSRNOP00000071327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
Rnor_6.0 Ensembl203,830,199 - 3,843,445 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085547   ⟹   ENSRNOP00000073041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
Rnor_6.0 Ensembl203,830,376 - 3,858,137 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,797,778 - 4,812,745 (-)Ensembl
Rnor_6.0 Ensembl205,314,442 - 5,329,279 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104091   ⟹   ENSRNOP00000079082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107648   ⟹   ENSRNOP00000082947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112730   ⟹   ENSRNOP00000097357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115128   ⟹   ENSRNOP00000080979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000120229   ⟹   ENSRNOP00000086235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,786,929 - 4,815,985 (-)Ensembl
RefSeq Acc Id: NM_212528   ⟹   NP_997693
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,929 - 4,815,789 (-)NCBI
Rnor_6.0203,830,164 - 3,859,022 (+)NCBI
Rnor_5.0205,908,541 - 5,938,415 (+)NCBI
RGSC_v3.4204,924,452 - 4,953,310 (-)RGD
Celera206,387,407 - 6,415,975 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255928   ⟹   XP_006255990
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,326 - 3,859,019 (+)NCBI
Rnor_5.0205,908,541 - 5,938,415 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255929   ⟹   XP_006255991
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,326 - 3,859,019 (+)NCBI
Rnor_5.0205,908,541 - 5,938,415 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772720   ⟹   XP_008770942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,324 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601580   ⟹   XP_017457069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,324 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601581   ⟹   XP_017457070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,326 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601582   ⟹   XP_017457071
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,324 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601583   ⟹   XP_017457072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,326 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601584   ⟹   XP_017457073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,326 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601585   ⟹   XP_017457074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
Rnor_6.0203,829,325 - 3,859,019 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098499   ⟹   XP_038954427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,809,857 (-)NCBI
RefSeq Acc Id: XM_039098500   ⟹   XP_038954428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,809,855 (-)NCBI
RefSeq Acc Id: XM_039098501   ⟹   XP_038954429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,808,273 (-)NCBI
RefSeq Acc Id: XM_039098502   ⟹   XP_038954430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,786,932 - 4,816,598 (-)NCBI
RefSeq Acc Id: XR_005497184
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,793,352 - 4,816,598 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_997693   ⟸   NM_212528
- Peptide Label: precursor
- UniProtKB: Q6MGB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255990   ⟸   XM_006255928
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006255991   ⟸   XM_006255929
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008770942   ⟸   XM_008772720
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017457069   ⟸   XM_017601580
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457071   ⟸   XM_017601582
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457074   ⟸   XM_017601585
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017457070   ⟸   XM_017601581
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457072   ⟸   XM_017601583
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457073   ⟸   XM_017601584
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000048846   ⟸   ENSRNOT00000045533
RefSeq Acc Id: ENSRNOP00000073041   ⟸   ENSRNOT00000085547
RefSeq Acc Id: ENSRNOP00000071327   ⟸   ENSRNOT00000084117
RefSeq Acc Id: XP_038954430   ⟸   XM_039098502
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038954427   ⟸   XM_039098499
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038954428   ⟸   XM_039098500
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038954429   ⟸   XM_039098501
- Peptide Label: isoform X12
RefSeq Acc Id: ENSRNOP00000080979   ⟸   ENSRNOT00000115128
RefSeq Acc Id: ENSRNOP00000082947   ⟸   ENSRNOT00000107648
RefSeq Acc Id: ENSRNOP00000086235   ⟸   ENSRNOT00000120229
RefSeq Acc Id: ENSRNOP00000097357   ⟸   ENSRNOT00000112730
RefSeq Acc Id: ENSRNOP00000079082   ⟸   ENSRNOT00000104091
Transcriptome

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

Promoters
RGD ID:13701321
Promoter ID:EPDNEW_R11842
Type:single initiation site
Name:Col11a2_1
Description:collagen type XI alpha 2 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_6.0203,830,199 - 3,830,259EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5912601 5912602 G A snv SHRSP/Gcrc (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), GK/Ox (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW)
20 5912628 5912629 G A snv GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), F344/Jcl (KyushuU), ZFDM (KyushuU), F344/Stm (KyushuU)
20 5930301 5930302 G A snv WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), F344/Jcl (KyushuU), ZFDM (KyushuU), F344/NRrrc (Illumina) (KNAW), LEW/NCrl (KNAW), LEW/Crl (KNAW), FHH/EurMcwi (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), SS/JrHsdMcwi (KNAW), SS/Jr (KNAW), SR/JrHsd (KNAW), LL/MavRrrc (KNAW), WN/N (KNAW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 4795043 4795044 C T snv LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), LL/MavRrrcAek (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WN/N (2020), WKY/NCrl (2019), WKY/N (2020), LEXF1C/Stm (2019)
20 4812654 4812655 C T snv WN/N (2020), WKY/N (2020), WKY/NCrl (2019), SR/JrHsd (2020), LL/MavRrrcAek (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), LEW/Crl (2019), FXLE18/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), SS/JrHsdMcwi (2019)
20 4812681 4812682 C T snv SHRSP/A3NCrl (2019), HXB31/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), GK/FarMcwi (2019), BXH2/CubMcwi (2020), SHR/OlalpcvMcwi (2019)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3833270 3833271 G A snv BXH2/CubMcwi (2020), GK/FarMcwi (2019), SHR/OlalpcvMcwi (2019), HXB31/IpcvMcwi (2019), SHRSP/A3NCrl (2019), HXB2/IpcvMcwi (2019)
20 3833297 3833298 G A snv GH/OmrMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LL/MavRrrcAek (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WKY/NCrl (2019), WKY/N (2020), WN/N (2020)
20 3849393 3849394 G A snv ACI/N (MCW), MR/N (MCW), M520/N (MCW), Buf/N (MCW)
20 3850905 3850906 G A snv ACI/N (MCW), M520/N (MCW)
20 3850906 3850907 C T snv F344/NRrrc (MCW), WKY/N (MCW), WN/N (MCW)
20 3850908 3850909 G A snv LEW/NCrlBR (RGD), LL/MavRrrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE18/Stm (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LL/MavRrrcAek (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019), WKY/NCrl (2019), WKY/N (2020), WN/N (2020), LEW/Crl (RGD), SS/JrHsdMcwi (MCW), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), SR/JrHsd (MCW)
20 3851966 3851967 G A snv F344/NRrrc (MCW), WN/N (MCW)
20 3852214 3852215 C A snv MR/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 4932566 4932567 C T snv FHH/EurMcwi (MCW), F344/NHsd (ICAHN), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MDC), F344/NRrrc (KNAW), WKY/N (KNAW), WN/N (KNAW), GH/OmrMcwi (MCW), F344/NCrl (ICL), FHH/EurMcwi (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LL/MavRrrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich)
20 4937634 4937635 T G snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2373 AgrOrtholog
Ensembl Genes ENSRNOG00000000463 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000061939 Ensembl
Ensembl Protein ENSRNOP00000048846 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071327 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073041 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000080979 ENTREZGENE
Ensembl Transcript ENSRNOT00000045533 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084117 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085547 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000115128 ENTREZGENE
InterPro Collagen UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
KEGG Report rno:294279 UniProtKB/TrEMBL
NCBI Gene 294279 ENTREZGENE
Pfam COLFI UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
PhenoGen Col11a2 PhenoGen
PROSITE NC1_FIB UniProtKB/TrEMBL
SMART COLFI UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
  TSPN UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt A0A0G2K069_RAT UniProtKB/TrEMBL
  F6T0B3_RAT UniProtKB/TrEMBL
  Q6MGB2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Col11a2  collagen type XI alpha 2 chain  LOC100911886  collagen alpha-2(XI) chain-like  Data Merged 737654 PROVISIONAL
2016-07-27 Col11a2  collagen type XI alpha 2 chain  Col11a2  collagen, type XI, alpha 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911886  collagen alpha-2(XI) chain-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-25 Col11a2  collagen, type XI, alpha 2  Col11a2  procollagen, type XI, alpha 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-03-29 Col11a2  procollagen, type XI, alpha 2  Col11a2_mapped  procollagen, type XI, alpha 2 (mapped)  Symbol and Name updated 1299863 APPROVED
2007-03-29 Col11a2_mapped  procollagen, type XI, alpha 2 (mapped)  Col11a2_retired  procollagen, type XI, alpha 2 (mapped)  Data Merged 737654 APPROVED
2007-03-29 Col11a2_retired    Col11a2  procollagen, type XI, alpha 2 (mapped)  Symbol updated 1299863 PROVISIONAL
2006-11-20 Col11a2  procollagen, type XI, alpha 2 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Col11a2_mapped  procollagen, type XI, alpha 2 (mapped)  Col11a2  procollagen, type XI, alpha 2  Symbol and Name updated 1556543 APPROVED
2002-11-06 Col11a2  procollagen, type XI, alpha 2    Type XI collagen, alpha2 chain  Name updated 625702 APPROVED
2002-06-10 Col11a2  Type XI collagen, alpha2 chain      Symbol and Name status set to approved 70586 APPROVED