Tlx3 (T-cell leukemia, homeobox 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Tlx3 (T-cell leukemia, homeobox 3) Rattus norvegicus
Analyze
Symbol: Tlx3
Name: T-cell leukemia, homeobox 3
RGD ID: 1564190
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in animal organ development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including nervous system development; regulation of respiratory gaseous exchange by nervous system process; and respiratory gaseous exchange by respiratory system. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human TLX3 (T cell leukemia homeobox 3); INTERACTS WITH 6-propyl-2-thiouracil; fipronil; sodium dichromate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC497881; RGD1564190; similar to HOX11L2; T-cell leukemia homeobox protein 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81018,293,932 - 18,296,551 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1018,293,932 - 18,296,773 (-)EnsemblGRCr8
mRatBN7.21017,789,706 - 17,792,207 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,790,053 - 17,792,207 (-)EnsemblmRatBN7.2
Rnor_6.01018,128,869 - 18,131,745 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1018,129,408 - 18,131,562 (-)Ensemblrn6Rnor6.0
Rnor_5.01018,012,959 - 18,015,778 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41018,100,105 - 18,102,910 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1017,429,807 - 17,432,683 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse:




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
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10700185   PMID:12023301   PMID:15064766   PMID:15229182   PMID:15466398   PMID:15527896   PMID:16234809   PMID:22787056  


Genomics

Comparative Map Data
Tlx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81018,293,932 - 18,296,551 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1018,293,932 - 18,296,773 (-)EnsemblGRCr8
mRatBN7.21017,789,706 - 17,792,207 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,790,053 - 17,792,207 (-)EnsemblmRatBN7.2
Rnor_6.01018,128,869 - 18,131,745 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1018,129,408 - 18,131,562 (-)Ensemblrn6Rnor6.0
Rnor_5.01018,012,959 - 18,015,778 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41018,100,105 - 18,102,910 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1017,429,807 - 17,432,683 (-)NCBICelera
Cytogenetic Map10q12NCBI
TLX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385171,309,248 - 171,312,139 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5171,309,248 - 171,312,139 (+)Ensemblhg38GRCh38
GRCh375170,736,252 - 170,739,143 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365170,668,893 - 170,671,743 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345170,668,892 - 170,671,742NCBI
Celera5166,768,846 - 166,771,694 (+)NCBICelera
Cytogenetic Map5q35.1NCBI
HuRef5165,834,169 - 165,837,074 (+)NCBIHuRef
CHM1_15170,168,866 - 170,171,714 (+)NCBICHM1_1
T2T-CHM13v2.05171,849,588 - 171,852,477 (+)NCBIT2T-CHM13v2.0
Tlx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391133,150,748 - 33,158,588 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1133,150,752 - 33,153,589 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381133,200,752 - 33,203,588 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1133,200,752 - 33,203,589 (-)Ensemblmm10GRCm38
MGSCv371133,100,752 - 33,103,588 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361133,101,279 - 33,103,459 (-)NCBIMGSCv36mm8
Celera1135,612,871 - 35,615,713 (-)NCBICelera
Cytogenetic Map11A4NCBI
cM Map1119.21NCBI
Tlx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540824,102,996 - 24,105,292 (+)Ensembl
ChiLan1.0NW_00495540824,103,123 - 24,105,292 (+)NCBIChiLan1.0ChiLan1.0
TLX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24166,446,166 - 166,449,091 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15164,585,708 - 164,588,633 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05166,658,166 - 166,661,098 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15173,411,881 - 173,414,639 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5173,411,881 - 173,414,106 (+)EnsemblpanPan2panpan1.1
TLX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1440,816,351 - 40,818,582 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl440,816,467 - 40,818,723 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha440,766,907 - 40,769,107 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0441,196,138 - 41,198,322 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl441,195,856 - 41,198,346 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1441,010,708 - 41,012,907 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0441,201,083 - 41,203,253 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0441,711,478 - 41,713,662 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tlx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721395,049,616 - 95,052,256 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366093,772,353 - 3,774,607 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366093,772,432 - 3,774,554 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TLX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1652,823,657 - 52,826,804 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11652,823,839 - 52,826,717 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21657,021,604 - 57,023,802 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TLX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12373,486,002 - 73,488,935 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2373,486,154 - 73,488,396 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660345,164,194 - 5,167,132 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tlx3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473318,759,941 - 18,762,854 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473318,760,060 - 18,762,909 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tlx3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v196,028,551 - 6,031,247 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tlx3
17 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:77
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000006676
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101774978420796344Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101576223019737486Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
1 9 62 12 7 5 5 4 24 14 53 4 29 2 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000006676   ⟹   ENSRNOP00000006676
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1018,293,932 - 18,296,773 (-)Ensembl
mRatBN7.2 Ensembl1017,790,053 - 17,792,207 (-)Ensembl
Rnor_6.0 Ensembl1018,129,408 - 18,131,562 (-)Ensembl
RefSeq Acc Id: NM_001427590   ⟹   NP_001414519
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81018,293,932 - 18,296,551 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414519 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAE92725 (Get FASTA)   NCBI Sequence Viewer  
  EDM04069 (Get FASTA)   NCBI Sequence Viewer  
  EDM04070 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006676
  ENSRNOP00000006676.6
Ensembl Acc Id: ENSRNOP00000006676   ⟸   ENSRNOT00000006676
RefSeq Acc Id: NP_001414519   ⟸   NM_001427590
- UniProtKB: A6HDG5 (UniProtKB/TrEMBL),   G3V6M6 (UniProtKB/TrEMBL)
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6M6-F1-model_v2 AlphaFold G3V6M6 1-291 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564190 AgrOrtholog
BioCyc Gene G2FUF-25606 BioCyc
Ensembl Genes ENSRNOG00000004976 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006676 ENTREZGENE
  ENSRNOT00000006676.8 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox_CS UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  TLX1/2/3 UniProtKB/TrEMBL
NCBI Gene 497881 ENTREZGENE
PANTHER PTHR45921 UniProtKB/TrEMBL
  T-CELL LEUKEMIA HOMEOBOX PROTEIN 3 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Tlx3 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004976 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6HDG5 ENTREZGENE, UniProtKB/TrEMBL
  G3V6M6 ENTREZGENE, UniProtKB/TrEMBL
  Q1XIC7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Tlx3  T-cell leukemia, homeobox 3  RGD1564190_predicted  similar to HOX11L2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564190_predicted  similar to HOX11L2 (predicted)  LOC497881  similar to HOX11L2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC497881  similar to HOX11L2      Symbol and Name status set to provisional 70820 PROVISIONAL