Ttc13 (tetratricopeptide repeat domain 13) - Rat Genome Database

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Gene: Ttc13 (tetratricopeptide repeat domain 13) Rattus norvegicus
Analyze
Symbol: Ttc13
Name: tetratricopeptide repeat domain 13
RGD ID: 1310186
Description: Orthologous to human TTC13 (tetratricopeptide repeat domain 13); INTERACTS WITH 2-methoxyethanol; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC292095; tetratricopeptide repeat protein 13
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21952,637,431 - 52,692,196 (-)NCBI
Rnor_6.0 Ensembl1957,429,980 - 57,484,742 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01957,429,980 - 57,484,583 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01968,135,050 - 68,189,367 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,848,488 - 54,904,567 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11954,853,541 - 54,909,433 (-)NCBI
Celera1952,006,329 - 52,060,544 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Ttc13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21952,637,431 - 52,692,196 (-)NCBI
Rnor_6.0 Ensembl1957,429,980 - 57,484,742 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01957,429,980 - 57,484,583 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01968,135,050 - 68,189,367 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41954,848,488 - 54,904,567 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11954,853,541 - 54,909,433 (-)NCBI
Celera1952,006,329 - 52,060,544 (-)NCBICelera
Cytogenetic Map19q12NCBI
TTC13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1230,906,243 - 230,978,875 (-)EnsemblGRCh38hg38GRCh38
GRCh381230,906,243 - 230,978,872 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371231,041,989 - 231,114,607 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361229,108,613 - 229,181,207 (-)NCBINCBI36hg18NCBI36
Build 341227,348,724 - 227,421,319NCBI
Celera1204,307,932 - 204,380,251 (-)NCBI
Cytogenetic Map1q42.2NCBI
HuRef1201,526,601 - 201,599,336 (-)NCBIHuRef
CHM1_11232,314,940 - 232,387,908 (-)NCBICHM1_1
Ttc13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398125,398,066 - 125,448,748 (-)NCBIGRCm39mm39
GRCm39 Ensembl8125,398,071 - 125,448,722 (-)Ensembl
GRCm388124,671,327 - 124,722,011 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8124,671,332 - 124,721,983 (-)EnsemblGRCm38mm10GRCm38
MGSCv378127,195,227 - 127,245,875 (-)NCBIGRCm37mm9NCBIm37
MGSCv368127,557,417 - 127,608,052 (-)NCBImm8
Celera8128,969,473 - 129,027,118 (-)NCBICelera
Cytogenetic Map8E2NCBI
Ttc13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554927,683,443 - 7,743,718 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554927,683,353 - 7,743,066 (+)NCBIChiLan1.0ChiLan1.0
TTC13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11211,481,786 - 211,536,834 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1211,481,786 - 211,536,837 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01206,454,877 - 206,527,628 (-)NCBIMhudiblu_PPA_v0panPan3
TTC13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.148,424,835 - 8,503,133 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl48,424,882 - 8,502,600 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha48,416,667 - 8,496,911 (+)NCBI
ROS_Cfam_1.048,450,010 - 8,529,676 (+)NCBI
UMICH_Zoey_3.148,453,507 - 8,533,827 (+)NCBI
UNSW_CanFamBas_1.048,575,523 - 8,655,844 (+)NCBI
UU_Cfam_GSD_1.048,805,639 - 8,885,928 (+)NCBI
Ttc13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934443,397,582 - 43,455,288 (+)NCBI
SpeTri2.0NW_00493648419,574,455 - 19,620,505 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTC13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1459,409,123 - 59,509,549 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11459,409,128 - 59,491,966 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21464,073,719 - 64,156,593 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TTC13
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12568,147,950 - 68,251,017 (-)NCBI
Ttc13
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477518,652,611 - 18,713,577 (+)NCBI

Position Markers
RH141350  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01957,430,162 - 57,430,362NCBIRnor6.0
Rnor_5.01968,135,232 - 68,135,432UniSTSRnor5.0
RGSC_v3.41954,848,670 - 54,848,870UniSTSRGSC3.4
Celera1952,006,511 - 52,006,711UniSTS
RH 3.4 Map19736.8UniSTS
Cytogenetic Map19q12UniSTS
BE107052  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01957,432,632 - 57,432,789NCBIRnor6.0
Rnor_5.01968,137,702 - 68,137,859UniSTSRnor5.0
RGSC_v3.41954,851,140 - 54,851,297UniSTSRGSC3.4
Celera1952,008,981 - 52,009,138UniSTS
RH 3.4 Map19723.4UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)195473521758072143Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:685
Count of miRNA genes:298
Interacting mature miRNAs:372
Transcripts:ENSRNOT00000025548
Prediction methods:Microtar, Miranda, Rnahybrid
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 3 29 49 40 18 40 67 28 33 8
Low 14 8 1 1 1 8 11 7 7 8 3 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001136162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC125724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY724473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC105871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025548   ⟹   ENSRNOP00000025548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1957,429,980 - 57,484,566 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079783   ⟹   ENSRNOP00000070958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1957,430,131 - 57,484,742 (-)Ensembl
RefSeq Acc Id: NM_001136162   ⟹   NP_001129634
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,431 - 52,692,183 (-)NCBI
Rnor_6.01957,429,980 - 57,484,566 (-)NCBI
Rnor_5.01968,135,050 - 68,189,367 (-)NCBI
RGSC_v3.41954,848,488 - 54,904,567 (-)RGD
Celera1952,006,329 - 52,060,544 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255802   ⟹   XP_006255864
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,599 - 52,692,196 (-)NCBI
Rnor_6.01957,430,148 - 57,484,583 (-)NCBI
Rnor_5.01968,135,050 - 68,189,367 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255803   ⟹   XP_006255865
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,607 - 52,692,162 (-)NCBI
Rnor_6.01957,430,148 - 57,484,583 (-)NCBI
Rnor_5.01968,135,050 - 68,189,367 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255805   ⟹   XP_006255867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,607 - 52,692,162 (-)NCBI
Rnor_6.01957,430,148 - 57,484,583 (-)NCBI
Rnor_5.01968,135,050 - 68,189,367 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601247   ⟹   XP_017456736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,599 - 52,692,196 (-)NCBI
Rnor_6.01957,430,148 - 57,484,583 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039097660   ⟹   XP_038953588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,607 - 52,692,196 (-)NCBI
RefSeq Acc Id: XM_039097661   ⟹   XP_038953589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,599 - 52,692,196 (-)NCBI
RefSeq Acc Id: XM_039097662   ⟹   XP_038953590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,599 - 52,692,162 (-)NCBI
RefSeq Acc Id: XM_039097663   ⟹   XP_038953591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,607 - 52,692,162 (-)NCBI
RefSeq Acc Id: XM_039097664   ⟹   XP_038953592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,599 - 52,665,706 (-)NCBI
RefSeq Acc Id: XM_039097665   ⟹   XP_038953593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21952,637,599 - 52,660,205 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001129634   ⟸   NM_001136162
- Peptide Label: precursor
- UniProtKB: F1LR77 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255865   ⟸   XM_006255803
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006255867   ⟸   XM_006255805
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006255864   ⟸   XM_006255802
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JZ94 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456736   ⟸   XM_017601247
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000070958   ⟸   ENSRNOT00000079783
RefSeq Acc Id: ENSRNOP00000025548   ⟸   ENSRNOT00000025548
RefSeq Acc Id: XP_038953589   ⟸   XM_039097661
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038953590   ⟸   XM_039097662
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953592   ⟸   XM_039097664
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038953593   ⟸   XM_039097665
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038953588   ⟸   XM_039097660
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038953591   ⟸   XM_039097663
- Peptide Label: isoform X8
Protein Domains
TPR_REGION

Transcriptome

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

Promoters
RGD ID:13701238
Promoter ID:EPDNEW_R11761
Type:multiple initiation site
Name:Ttc13_1
Description:tetratricopeptide repeat domain 13
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_6.01957,484,555 - 57,484,615EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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)
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
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 (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)
Visual CSV TAB Printer
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)
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
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)
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)
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
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/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
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 (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
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
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
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
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
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 (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
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)
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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/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
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 (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 (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
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 (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 (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 (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
19 68146399 68146400 T G snv ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 54861059 54861060 T G snv ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310186 AgrOrtholog
Ensembl Genes ENSRNOG00000018884 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025548 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070958 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025548 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079783 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7379040 IMAGE-MGC_LOAD
  IMAGE:7443849 IMAGE-MGC_LOAD
InterPro TPR-contain_dom UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
  TPR_1 UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
KEGG Report rno:292095 UniProtKB/TrEMBL
MGC_CLONE MGC:112895 IMAGE-MGC_LOAD
  MGC:125081 IMAGE-MGC_LOAD
NCBI Gene 292095 ENTREZGENE
Pfam TPR_1 UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Ttc13 PhenoGen
PROSITE TPR UniProtKB/TrEMBL
  TPR_REGION UniProtKB/TrEMBL
SMART TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A0G2JZ94 ENTREZGENE, UniProtKB/TrEMBL
  F1LR77 ENTREZGENE, UniProtKB/TrEMBL
  Q3KR69_RAT UniProtKB/TrEMBL
  Q4G015_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Ttc13  tetratricopeptide repeat domain 13  Ttc13_predicted  tetratricopeptide repeat domain 13 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ttc13_predicted  tetratricopeptide repeat domain 13 (predicted)      Symbol and Name status set to approved 70820 APPROVED