Col13a1 (collagen type XIII alpha 1 chain) - Rat Genome Database

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Gene: Col13a1 (collagen type XIII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col13a1
Name: collagen type XIII alpha 1 chain
RGD ID: 1595704
Description: Predicted to enable heparin binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in several processes, including cell-matrix adhesion; collagen fibril organization; and notochord development. Predicted to act upstream of or within endochondral ossification. Predicted to be part of collagen trimer. Predicted to be active in cell-cell junction; extracellular matrix; and extracellular space. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 19. Orthologous to human COL13A1 (collagen type XIII alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; cobalt dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: collagen alpha-1(XIII) chain; collagen, type XIII, alpha 1; LOC499431; procollagen, type XIII, alpha 1; similar to alpha 1 type XIII collagen isoform 17
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
mRatBN7.22029,783,965 - 29,924,116 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2029,783,965 - 29,924,032 (-)Ensembl
Rnor_6.02031,456,502 - 31,598,360 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,456,852 - 31,598,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02033,254,962 - 33,395,070 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,208,654 - 29,348,751 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2031,209,120 - 31,348,066 (-)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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:10865988   PMID:11470398   PMID:11956183   PMID:12477932  


Genomics

Comparative Map Data
Col13a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22029,783,965 - 29,924,116 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2029,783,965 - 29,924,032 (-)Ensembl
Rnor_6.02031,456,502 - 31,598,360 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2031,456,852 - 31,598,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02033,254,962 - 33,395,070 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,208,654 - 29,348,751 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2031,209,120 - 31,348,066 (-)NCBICelera
Cytogenetic Map20q11NCBI
COL13A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1069,801,880 - 69,964,275 (+)EnsemblGRCh38hg38GRCh38
GRCh381069,801,835 - 69,959,144 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371071,561,662 - 71,718,900 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361071,231,650 - 71,388,909 (+)NCBINCBI36hg18NCBI36
Celera1064,838,564 - 64,996,131 (+)NCBI
Cytogenetic Map10q22.1NCBI
HuRef1065,553,122 - 65,710,673 (+)NCBIHuRef
CHM1_11071,843,392 - 72,000,665 (+)NCBICHM1_1
Col13a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391061,674,013 - 61,814,985 (-)NCBIGRCm39mm39
GRCm39 Ensembl1061,674,015 - 61,814,887 (-)Ensembl
GRCm381061,838,234 - 61,979,206 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1061,838,236 - 61,979,108 (-)EnsemblGRCm38mm10GRCm38
MGSCv371061,301,246 - 61,441,856 (-)NCBIGRCm37mm9NCBIm37
MGSCv361061,233,855 - 61,374,465 (-)NCBImm8
Celera1062,940,611 - 63,081,159 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.29NCBI
Col13a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543721,256,636 - 21,392,814 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543721,256,410 - 21,393,385 (-)NCBIChiLan1.0ChiLan1.0
COL13A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11068,806,841 - 68,964,088 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1068,807,425 - 68,963,642 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01066,277,302 - 66,434,410 (+)NCBIMhudiblu_PPA_v0panPan3
COL13A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1420,838,163 - 20,987,412 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl420,837,650 - 20,986,962 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha420,971,110 - 21,119,964 (+)NCBI
ROS_Cfam_1.0421,113,705 - 21,262,719 (+)NCBI
UMICH_Zoey_3.1421,012,409 - 21,161,238 (+)NCBI
UNSW_CanFamBas_1.0421,216,918 - 21,365,710 (+)NCBI
UU_Cfam_GSD_1.0421,561,379 - 21,710,027 (+)NCBI
Col13a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721360,100,636 - 60,239,816 (-)NCBI
SpeTri2.0NW_0049365218,588,568 - 8,643,786 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL13A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1472,787,502 - 72,953,096 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11472,786,780 - 72,953,093 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21478,706,033 - 78,871,075 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL13A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1961,342,482 - 61,500,072 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl961,344,481 - 61,499,539 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604822,080,101 - 22,237,649 (-)NCBIVero_WHO_p1.0
Col13a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247544,016,873 - 4,163,065 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D20Got30  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,843,196 - 29,843,387 (+)MAPPERmRatBN7.2
Rnor_6.02031,515,735 - 31,515,923NCBIRnor6.0
Rnor_5.02033,313,286 - 33,313,474UniSTSRnor5.0
RGSC_v3.42029,267,613 - 29,267,802RGDRGSC3.4
RGSC_v3.42029,267,614 - 29,267,802UniSTSRGSC3.4
RGSC_v3.12029,281,413 - 29,281,602RGD
Celera2031,268,035 - 31,268,223UniSTS
Cytogenetic Map20q11UniSTS
RH144219  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,923,658 - 29,923,818 (+)MAPPERmRatBN7.2
Rnor_6.02031,597,925 - 31,598,084NCBIRnor6.0
Rnor_5.02033,394,668 - 33,394,827UniSTSRnor5.0
RGSC_v3.42029,348,378 - 29,348,537UniSTSRGSC3.4
Celera2031,347,693 - 31,347,852UniSTS
Cytogenetic Map20q11UniSTS
BI275884  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,819,586 - 29,819,757 (+)MAPPERmRatBN7.2
Rnor_6.02031,492,123 - 31,492,293NCBIRnor6.0
Rnor_5.02033,289,746 - 33,289,916UniSTSRnor5.0
RGSC_v3.42029,244,031 - 29,244,201UniSTSRGSC3.4
Celera2031,244,547 - 31,244,717UniSTS
Cytogenetic Map20q11UniSTS
AU048925  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22029,864,779 - 29,864,967 (+)MAPPERmRatBN7.2
Rnor_6.02031,537,314 - 31,537,501NCBIRnor6.0
Rnor_5.02033,334,865 - 33,335,052UniSTSRnor5.0
RGSC_v3.42029,289,193 - 29,289,380UniSTSRGSC3.4
Celera2031,289,568 - 31,289,755UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:140
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000046537
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 12 4 4 4 20 23 11
Low 3 28 52 37 18 37 6 9 74 15 15 6
Below cutoff 3 1 1 2 2 3 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001109172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008772912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC162018 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474016 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000046537   ⟹   ENSRNOP00000042926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,785,785 - 29,924,032 (-)Ensembl
Rnor_6.0 Ensembl2031,456,852 - 31,598,118 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085877   ⟹   ENSRNOP00000072337
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,783,965 - 29,924,032 (-)Ensembl
Rnor_6.0 Ensembl2031,458,322 - 31,597,830 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098211   ⟹   ENSRNOP00000084135
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,783,965 - 29,924,032 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102397   ⟹   ENSRNOP00000083370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,783,965 - 29,924,032 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107190   ⟹   ENSRNOP00000087411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2029,783,965 - 29,924,032 (-)Ensembl
RefSeq Acc Id: NM_001109172   ⟹   NP_001102642
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,783,965 - 29,924,032 (-)NCBI
Rnor_6.02031,456,502 - 31,598,298 (-)NCBI
Rnor_5.02033,254,962 - 33,395,070 (-)NCBI
RGSC_v3.42029,208,654 - 29,348,751 (-)RGD
Celera2031,209,120 - 31,348,066 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256470   ⟹   XP_006256532
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
Rnor_6.02031,458,371 - 31,598,359 (-)NCBI
Rnor_5.02033,254,962 - 33,395,070 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256481   ⟹   XP_006256543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,783,965 - 29,924,114 (-)NCBI
Rnor_6.02031,456,502 - 31,598,358 (-)NCBI
Rnor_5.02033,254,962 - 33,395,070 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772904   ⟹   XP_008771126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
Rnor_6.02031,458,371 - 31,598,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008772910   ⟹   XP_008771132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
Rnor_6.02031,458,371 - 31,598,359 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099015   ⟹   XP_038954943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099016   ⟹   XP_038954944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099017   ⟹   XP_038954945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099018   ⟹   XP_038954946
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,114 (-)NCBI
RefSeq Acc Id: XM_039099019   ⟹   XP_038954947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099020   ⟹   XP_038954948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099021   ⟹   XP_038954949
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099023   ⟹   XP_038954951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,785,831 - 29,924,116 (-)NCBI
RefSeq Acc Id: XM_039099024   ⟹   XP_038954952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22029,783,965 - 29,924,114 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102642   ⟸   NM_001109172
- UniProtKB: A0A0G2K2Q8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256543   ⟸   XM_006256481
- Peptide Label: isoform X13
- UniProtKB: B1WC63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256532   ⟸   XM_006256470
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008771132   ⟸   XM_008772910
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008771126   ⟸   XM_008772904
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000042926   ⟸   ENSRNOT00000046537
RefSeq Acc Id: ENSRNOP00000072337   ⟸   ENSRNOT00000085877
RefSeq Acc Id: XP_038954952   ⟸   XM_039099024
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038954951   ⟸   XM_039099023
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038954947   ⟸   XM_039099019
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038954948   ⟸   XM_039099020
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038954944   ⟸   XM_039099016
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954945   ⟸   XM_039099017
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954949   ⟸   XM_039099021
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038954943   ⟸   XM_039099015
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954946   ⟸   XM_039099018
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000087411   ⟸   ENSRNOT00000107190
RefSeq Acc Id: ENSRNOP00000083370   ⟸   ENSRNOT00000102397
RefSeq Acc Id: ENSRNOP00000084135   ⟸   ENSRNOT00000098211

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
ACI/N (2020)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
LEW/Crl (2019)
Visual CSV TAB Printer
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)
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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
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)
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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SBN/Ygl (MCW)
Visual CSV TAB Printer
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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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)
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
WKY/N (2020)
Visual CSV TAB Printer
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)
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595704 AgrOrtholog
Ensembl Genes ENSRNOG00000000552 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042926 UniProtKB/TrEMBL
  ENSRNOP00000072337 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046537 UniProtKB/TrEMBL
  ENSRNOT00000085877 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9098304 IMAGE-MGC_LOAD
InterPro Collagen UniProtKB/TrEMBL
KEGG Report rno:499431 UniProtKB/TrEMBL
MGC_CLONE MGC:187895 IMAGE-MGC_LOAD
NCBI Gene 499431 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
PhenoGen Col13a1 PhenoGen
UniProt A0A0G2K2Q8 ENTREZGENE, UniProtKB/TrEMBL
  B1WC63 ENTREZGENE, UniProtKB/TrEMBL
  D3ZSF4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col13a1  collagen type XIII alpha 1 chain  Col13a1  collagen, type XIII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Col13a1  collagen, type XIII, alpha 1  LOC499431  similar to alpha 1 type XIII collagen isoform 17  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC499431  similar to alpha 1 type XIII collagen isoform 17      Symbol and Name status set to provisional 70820 PROVISIONAL