Tshz1 (teashirt zinc finger homeobox 1) - Rat Genome Database
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Gene: Tshz1 (teashirt zinc finger homeobox 1) Rattus norvegicus
Analyze
Symbol: Tshz1
Name: teashirt zinc finger homeobox 1
RGD ID: 1311684
Description: Predicted to have DNA binding activity and metal ion binding activity. Predicted to be involved in anterior/posterior pattern specification; middle ear morphogenesis; and soft palate development. Orthologous to human TSHZ1 (teashirt zinc finger homeobox 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC307217; LOW QUALITY PROTEIN: teashirt homolog 1; Sdccag33; serologically defined colon cancer antigen 33; teashirt homolog 1; teashirt zinc finger family member 1
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
mRatBN7.21877,376,399 - 77,452,315 (-)NCBI
Rnor_6.0 Ensembl1880,862,372 - 80,865,584 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01880,860,995 - 80,907,744 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01879,910,848 - 79,956,064 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41880,536,036 - 80,541,518 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11880,610,862 - 80,619,594 (-)NCBI
Celera1875,999,997 - 76,045,459 (-)NCBICelera
Cytogenetic Map18q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

Molecular Function

References

Additional References at PubMed
PMID:17586487  


Genomics

Comparative Map Data
Tshz1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21877,376,399 - 77,452,315 (-)NCBI
Rnor_6.0 Ensembl1880,862,372 - 80,865,584 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01880,860,995 - 80,907,744 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01879,910,848 - 79,956,064 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41880,536,036 - 80,541,518 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11880,610,862 - 80,619,594 (-)NCBI
Celera1875,999,997 - 76,045,459 (-)NCBICelera
Cytogenetic Map18q12.3NCBI
TSHZ1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1875,210,755 - 75,289,950 (+)EnsemblGRCh38hg38GRCh38
GRCh381875,210,797 - 75,289,946 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371872,922,752 - 73,001,899 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371872,922,710 - 73,001,905 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361871,051,719 - 71,130,889 (+)NCBINCBI36hg18NCBI36
Build 341871,125,160 - 71,130,665NCBI
Celera1869,741,400 - 69,820,597 (+)NCBI
Cytogenetic Map18q22.3NCBI
HuRef1869,607,516 - 69,686,785 (+)NCBIHuRef
CHM1_11872,917,366 - 72,997,125 (+)NCBICHM1_1
Tshz1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391884,029,752 - 84,105,833 (-)NCBIGRCm39mm39
GRCm381884,011,627 - 84,087,708 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1884,011,627 - 84,087,706 (-)EnsemblGRCm38mm10GRCm38
MGSCv371884,181,019 - 84,255,954 (-)NCBIGRCm37mm9NCBIm37
MGSCv361884,145,820 - 84,220,755 (-)NCBImm8
Celera1885,079,396 - 85,154,615 (-)NCBICelera
Cytogenetic Map18E4NCBI
cM Map1857.53NCBI
Tshz1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540258,695,150 - 58,717,926 (+)NCBIChiLan1.0ChiLan1.0
TSHZ1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11871,873,600 - 71,951,654 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1871,873,594 - 71,951,654 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01868,597,354 - 68,676,462 (+)NCBIMhudiblu_PPA_v0panPan3
TSHZ1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl14,226,210 - 4,246,762 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.114,224,875 - 4,229,755 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tshz1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366163,353,334 - 3,378,819 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TSHZ1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1148,902,346 - 148,984,832 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11148,905,179 - 148,984,984 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21164,830,580 - 164,837,213 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TSHZ1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1184,622,407 - 4,702,267 (-)NCBI
ChlSab1.1 Ensembl184,623,731 - 4,626,925 (-)Ensembl
Tshz1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248065,389,464 - 5,463,222 (-)NCBI

Position Markers
D18Rat119  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01880,889,356 - 80,889,486NCBIRnor6.0
Rnor_5.01879,937,676 - 79,937,806UniSTSRnor5.0
RGSC_v3.41880,564,011 - 80,564,142RGDRGSC3.4
RGSC_v3.41880,564,012 - 80,564,142UniSTSRGSC3.4
RGSC_v3.11880,637,461 - 80,637,592RGD
Celera1876,027,071 - 76,027,201UniSTS
RH 2.0 Map1857.9RGD
SHRSP x BN Map1848.9499RGD
FHH x ACI Map1861.84RGD
Cytogenetic Map18q12.3UniSTS
RH102961  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01880,860,997 - 80,861,195NCBIRnor6.0
Rnor_5.01879,910,850 - 79,911,048UniSTSRnor5.0
RGSC_v3.41880,536,038 - 80,536,236UniSTSRGSC3.4
Celera1875,999,999 - 76,000,197UniSTS
Cytogenetic Map18q12.3UniSTS
BE120868  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01880,861,194 - 80,861,346NCBIRnor6.0
Rnor_5.01879,911,047 - 79,911,199UniSTSRnor5.0
RGSC_v3.41880,536,235 - 80,536,387UniSTSRGSC3.4
Celera1876,000,196 - 76,000,348UniSTS
RH 3.4 Map18814.3UniSTS
Cytogenetic Map18q12.3UniSTS
AU047890  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01880,896,550 - 80,896,751NCBIRnor6.0
Rnor_5.01879,944,870 - 79,945,071UniSTSRnor5.0
RGSC_v3.41880,571,206 - 80,571,407UniSTSRGSC3.4
Celera1876,034,265 - 76,034,466UniSTS
Cytogenetic Map18q12.3UniSTS
BF409889  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01880,928,739 - 80,928,912NCBIRnor6.0
Rnor_5.01879,977,059 - 79,977,232UniSTSRnor5.0
RGSC_v3.41880,603,395 - 80,603,568UniSTSRGSC3.4
Celera1876,066,258 - 76,066,431UniSTS
RH 3.4 Map18815.8UniSTS
Cytogenetic Map18q12.3UniSTS
ha3102  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01880,882,835 - 80,884,321NCBIRnor6.0
Rnor_6.01885,444,046 - 85,445,246NCBIRnor6.0
Rnor_5.01884,495,732 - 84,496,932UniSTSRnor5.0
Rnor_5.01879,931,482 - 79,932,968UniSTSRnor5.0
Cytogenetic Map18q12.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181569587287080053Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181569587287080053Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)182028575887080053Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260373687074531Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182596102681761656Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183267035287080053Rat
631518Bw11Body weight QTL 112.8body mass (VT:0001259)body weight (CMO:0000012)183822191983221919Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)184037576985375769Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184500219488201929Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184631947688201929Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184913092088201929Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184913092088201929Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184913092088201929Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)185137581688201929Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185137581688201929Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185303349487080053Rat
1558649Bw58Body weight QTL 583.40.0005body mass (VT:0001259)body weight (CMO:0000012)185744867888201929Rat
6893359Bw103Body weight QTL 1031.20.12body mass (VT:0001259)body weight (CMO:0000012)185744867888201929Rat
6893368Bw107Body weight QTL 1070.30.5body mass (VT:0001259)body weight (CMO:0000012)185744867888201929Rat
1298072Cia26Collagen induced arthritis QTL 263.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)185819630088201929Rat
6903356Bp354Blood pressure QTL 3544.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)186198564888201929Rat
724542Kidm2Kidney mass QTL 22.6kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)186300981288201929Rat
634333Pia19Pristane induced arthritis QTL 193.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)187715130183366399Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:61
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000021750
Prediction methods: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 3 17 23 11 9 11 71 35 34 11
Low 26 34 30 10 30 8 11 3 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021750   ⟹   ENSRNOP00000055055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1880,862,372 - 80,865,584 (-)Ensembl
RefSeq Acc Id: XM_008772238   ⟹   XP_008770460
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01880,860,995 - 80,907,744 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017587810   ⟹   XP_017443299
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1875,999,997 - 76,045,459 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039097340   ⟹   XP_038953268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21877,376,399 - 77,452,315 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038953268 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75193 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_008770460   ⟸   XM_008772238
- Sequence:
RefSeq Acc Id: XP_017443299   ⟸   XM_017587810
- Sequence:
RefSeq Acc Id: ENSRNOP00000055055   ⟸   ENSRNOT00000021750
RefSeq Acc Id: XP_038953268   ⟸   XM_039097340
Protein Domains
C2H2-type

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 (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)
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/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
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
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 (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311684 AgrOrtholog
Ensembl Genes ENSRNOG00000016246 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000055055 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021750 UniProtKB/TrEMBL
InterPro Homeobox_dom UniProtKB/TrEMBL
  Teashirt_fam UniProtKB/TrEMBL
  Tshz1 UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/TrEMBL
NCBI Gene 307217 ENTREZGENE
PANTHER PTHR12487 UniProtKB/TrEMBL
  PTHR12487:SF6 UniProtKB/TrEMBL
PhenoGen Tshz1 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
UniProt F1LW29_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Tshz1  teashirt zinc finger homeobox 1  Tshz1  teashirt zinc finger family member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Tshz1  teashirt zinc finger family member 1  Sdccag33_predicted  serologically defined colon cancer antigen 33 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Sdccag33_predicted  serologically defined colon cancer antigen 33 (predicted)      Symbol and Name status set to approved 70820 APPROVED