Zhx3 (zinc fingers and homeoboxes 3) - Rat Genome Database
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Gene: Zhx3 (zinc fingers and homeoboxes 3) Rattus norvegicus
Analyze
Symbol: Zhx3
Name: zinc fingers and homeoboxes 3
RGD ID: 631431
Description: Exhibits DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Localizes to nucleus. Orthologous to human ZHX3 (zinc fingers and homeoboxes 3); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Tix1; triple homeobox 1; zinc finger and homeodomain protein 3; zinc fingers and homeoboxes protein 3
Orthologs:
Homo sapiens (human) : ZHX3 (zinc fingers and homeoboxes 3)  HGNC  Alliance
Mus musculus (house mouse) : Zhx3 (zinc fingers and homeoboxes 3)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Zhx3 (zinc fingers and homeoboxes 3)
Pan paniscus (bonobo/pygmy chimpanzee) : ZHX3 (zinc fingers and homeoboxes 3)
Canis lupus familiaris (dog) : ZHX3 (zinc fingers and homeoboxes 3)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Zhx3 (zinc fingers and homeoboxes 3)
Sus scrofa (pig) : ZHX3 (zinc fingers and homeoboxes 3)
Chlorocebus sabaeus (African green monkey) : ZHX3 (zinc fingers and homeoboxes 3)
Heterocephalus glaber (naked mole-rat) : Zhx3 (zinc fingers and homeoboxes 3)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.03156,759,820 - 156,868,173 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3156,764,751 - 156,777,999 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03162,989,355 - 163,095,228 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43151,560,440 - 151,574,257 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13151,478,388 - 151,479,956 (-)NCBI
Celera3148,096,662 - 148,110,463 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:21174497  


Genomics

Comparative Map Data
Zhx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.03156,759,820 - 156,868,173 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3156,764,751 - 156,777,999 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03162,989,355 - 163,095,228 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43151,560,440 - 151,574,257 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13151,478,388 - 151,479,956 (-)NCBI
Celera3148,096,662 - 148,110,463 (-)NCBICelera
Cytogenetic Map3q42NCBI
ZHX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2041,178,448 - 41,317,672 (-)EnsemblGRCh38hg38GRCh38
GRCh382041,178,450 - 41,317,731 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372039,807,089 - 39,928,766 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362039,240,503 - 39,362,153 (-)NCBINCBI36hg18NCBI36
Build 342039,240,502 - 39,362,153NCBI
Celera2036,517,656 - 36,639,406 (-)NCBI
Cytogenetic Map20q12NCBI
HuRef2036,545,141 - 36,666,992 (-)NCBIHuRef
CHM1_12039,711,487 - 39,833,056 (-)NCBICHM1_1
Zhx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392160,612,367 - 160,714,910 (-)NCBI
GRCm382160,770,447 - 160,872,990 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2160,748,708 - 160,872,998 (-)EnsemblGRCm38mm10GRCm38
MGSCv372160,596,183 - 160,698,726 (-)NCBIGRCm37mm9NCBIm37
MGSCv362160,461,888 - 160,564,431 (-)NCBImm8
Celera2166,702,506 - 166,803,659 (-)NCBICelera
Cytogenetic Map2H2NCBI
Zhx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544515,632,995 - 15,785,238 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544515,632,723 - 15,785,238 (+)NCBIChiLan1.0ChiLan1.0
ZHX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12038,617,878 - 38,738,631 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2038,621,651 - 38,755,797 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02037,518,569 - 37,659,417 (-)NCBIMhudiblu_PPA_v0panPan3
ZHX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2429,223,236 - 29,282,171 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12429,217,434 - 29,343,475 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Zhx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936561464,443 - 596,604 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZHX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1743,848,350 - 43,962,992 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11743,848,345 - 43,963,084 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21749,248,058 - 49,252,810 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ZHX3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl222,456,123 - 22,590,134 (+)Ensembl
ChlSab1.1222,508,177 - 22,596,855 (+)NCBI
Zhx3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249191,802,708 - 1,972,676 (-)NCBI

Position Markers
RH137720  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03156,764,897 - 156,765,027NCBIRnor6.0
Rnor_5.03162,994,432 - 162,994,562UniSTSRnor5.0
RGSC_v3.43151,560,588 - 151,560,718UniSTSRGSC3.4
Celera3148,096,810 - 148,096,940UniSTS
Cytogenetic Map3q42UniSTS
RH 3.4 Map31368.1UniSTS
RH137781  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03156,767,934 - 156,768,177NCBIRnor6.0
Rnor_5.03162,997,469 - 162,997,712UniSTSRnor5.0
RGSC_v3.43151,563,625 - 151,563,868UniSTSRGSC3.4
Celera3148,099,847 - 148,100,090UniSTS
Cytogenetic Map3q42UniSTS
RH 3.4 Map31365.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153381237174632112Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3153381237174632112Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3153381237174632112Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3153381237174632112Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3153381237174632112Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3153381237174632112Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3153381237174632112Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153412455165355668Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)3153412455170534769Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3156381661176418101Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:269
Count of miRNA genes:168
Interacting mature miRNAs:200
Transcripts:ENSRNOT00000032588
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 2 29 14 16 14 6 6 64 29 28 11 6
Low 3 41 28 27 3 27 2 5 10 6 13 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000032588   ⟹   ENSRNOP00000034076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3156,764,751 - 156,777,999 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091208   ⟹   ENSRNOP00000073211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3156,774,313 - 156,777,999 (-)Ensembl
RefSeq Acc Id: NM_001047097   ⟹   NP_001040562
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,764,749 - 156,777,999 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
RGSC_v3.43151,560,440 - 151,574,257 (-)RGD
Celera3148,096,662 - 148,110,463 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235474   ⟹   XP_006235536
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,860,317 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235475   ⟹   XP_006235537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,868,173 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235476   ⟹   XP_006235538
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,867,921 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235477   ⟹   XP_006235539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,823,465 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235478   ⟹   XP_006235540
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,843,299 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235480   ⟹   XP_006235542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,868,173 (-)NCBI
Rnor_5.03162,989,355 - 163,095,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762344   ⟹   XP_008760566
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,759,820 - 156,868,172 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591788   ⟹   XP_017447277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03156,774,968 - 156,810,886 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001040562   ⟸   NM_001047097
- UniProtKB: Q80Z36 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235542   ⟸   XM_006235480
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235537   ⟸   XM_006235475
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235538   ⟸   XM_006235476
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235536   ⟸   XM_006235474
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235540   ⟸   XM_006235478
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006235539   ⟸   XM_006235477
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008760566   ⟸   XM_008762344
- Peptide Label: isoform X2
- UniProtKB: Q80Z36 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017447277   ⟸   XM_017591788
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000034076   ⟸   ENSRNOT00000032588
RefSeq Acc Id: ENSRNOP00000073211   ⟸   ENSRNOT00000091208
Protein Domains
Homeobox

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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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
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:631431 AgrOrtholog
Ensembl Genes ENSRNOG00000027988 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034076 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073211 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032588 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091208 UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/Swiss-Prot
  Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/Swiss-Prot
  Homez_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZHX_Znf_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:311604 UniProtKB/Swiss-Prot
NCBI Gene 311604 ENTREZGENE
Pfam Homeobox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homez UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf_C2H2_ZHX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zhx3 PhenoGen
PROSITE HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.225061 ENTREZGENE
UniProt A0A0G2K4X5_RAT UniProtKB/TrEMBL
  Q80Z36 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q1I1B1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Zhx3  zinc fingers and homeoboxes 3  Tix1  triple homeobox 1  Symbol and Name updated 1299863 APPROVED
2004-02-11 Tix1  triple homeobox 1      Symbol and Name status set to approved 625702 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized in nuclei 634246
gene_function transcriptional repressor that functions as a dimer 634246