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

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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 RNA polymerase II cis-regulatory region sequence-specific 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: MODEL
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21017,789,706 - 17,792,207 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,790,053 - 17,792,207 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01018,128,869 - 18,131,745 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1018,129,408 - 18,131,562 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01018,012,959 - 18,015,778 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41018,100,105 - 18,102,910 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1017,429,807 - 17,432,683 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
mRatBN7.21017,789,706 - 17,792,207 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,790,053 - 17,792,207 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01018,128,869 - 18,131,745 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1018,129,408 - 18,131,562 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01018,012,959 - 18,015,778 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41018,100,105 - 18,102,910 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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.p13 Ensembl5171,309,248 - 171,312,139 (+)EnsemblGRCh38hg38GRCh38
GRCh375170,736,252 - 170,739,143 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365170,668,893 - 170,671,743 (+)NCBINCBI36Build 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 Ensembl
GRCm381133,200,752 - 33,203,588 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1133,200,752 - 33,203,589 (-)EnsemblGRCm38mm10GRCm38
MGSCv371133,100,752 - 33,103,588 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361133,101,279 - 33,103,459 (-)NCBIMGSCv36mm8
Celera1135,612,871 - 35,615,713 (-)NCBICelera
Cytogenetic Map11A4NCBI
Tlx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540824,102,996 - 24,105,292 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540824,103,123 - 24,105,292 (+)NCBIChiLan1.0ChiLan1.0
TLX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15173,411,881 - 173,414,639 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5173,411,881 - 173,414,106 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05166,658,166 - 166,661,098 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha440,766,907 - 40,769,107 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0441,196,138 - 41,198,322 (-)NCBIROS_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_1.0
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
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473318,760,060 - 18,762,909 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tlx3
12 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101724551319388279Rat


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

endocrine system exocrine system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4
Low 41 7
Below cutoff 4 4 4 1 1 3 2 11 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006676   ⟹   ENSRNOP00000006676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,790,053 - 17,792,207 (-)Ensembl
Rnor_6.0 Ensembl1018,129,408 - 18,131,562 (-)Ensembl
RefSeq Acc Id: XM_573065   ⟹   XP_573065
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21017,789,706 - 17,792,207 (-)NCBI
Rnor_6.01018,128,869 - 18,131,745 (-)NCBI
Rnor_5.01018,012,959 - 18,015,778 (-)NCBI
RGSC_v3.41018,100,105 - 18,102,910 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_573065 (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  
Reference Sequences
RefSeq Acc Id: XP_573065   ⟸   XM_573065
- UniProtKB: G3V6M6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006676   ⟸   ENSRNOT00000006676
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 Protein ENSRNOP00000006676 ENTREZGENE
  ENSRNOP00000006676.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006676 ENTREZGENE
  ENSRNOT00000006676.7 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
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Tlx3 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt 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