Tcta (T-cell leukemia translocation altered) - Rat Genome Database

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Gene: Tcta (T-cell leukemia translocation altered) Rattus norvegicus
Analyze
Symbol: Tcta
Name: T-cell leukemia translocation altered
RGD ID: 1359333
Description: Predicted to be involved in negative regulation of osteoclast differentiation and osteoclast fusion. Predicted to be located in membrane. Orthologous to human TCTA (T cell leukemia translocation altered); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC306587; similar to RIKEN cDNA 9130410M22; T-cell leukemia translocation altered gene; T-cell leukemia translocation-altered gene protein homolog
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
GRCr88117,867,153 - 117,871,132 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8117,867,153 - 117,871,331 (-)EnsemblGRCr8
mRatBN7.28108,988,588 - 108,992,324 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,988,590 - 108,991,564 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8114,615,748 - 114,618,708 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,815,072 - 112,818,032 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08110,657,711 - 110,660,671 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08117,079,094 - 117,082,338 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,079,095 - 117,082,162 (-)Ensemblrn6Rnor6.0
Rnor_5.08116,427,898 - 116,431,164 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera8108,291,610 - 108,294,678 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Cloning and characterization of TCTA, a gene located at the site of a t(1;3) translocation. Aplan PD, etal., Cancer Res 1995 May 1;55(9):1917-21.
2. 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.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:19560569  


Genomics

Comparative Map Data
Tcta
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88117,867,153 - 117,871,132 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl8117,867,153 - 117,871,331 (-)EnsemblGRCr8
mRatBN7.28108,988,588 - 108,992,324 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,988,590 - 108,991,564 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx8114,615,748 - 114,618,708 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,815,072 - 112,818,032 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08110,657,711 - 110,660,671 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.08117,079,094 - 117,082,338 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,079,095 - 117,082,162 (-)Ensemblrn6Rnor6.0
Rnor_5.08116,427,898 - 116,431,164 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera8108,291,610 - 108,294,678 (-)NCBICelera
Cytogenetic Map8q32NCBI
TCTA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38349,412,423 - 49,416,476 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl349,412,212 - 49,416,476 (+)Ensemblhg38GRCh38
GRCh37349,449,856 - 49,453,909 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36349,424,643 - 49,428,913 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34349,424,642 - 49,428,912NCBI
Celera349,414,426 - 49,418,696 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef349,509,361 - 49,513,631 (+)NCBIHuRef
CHM1_1349,402,406 - 49,406,676 (+)NCBICHM1_1
T2T-CHM13v2.0349,441,802 - 49,445,855 (+)NCBIT2T-CHM13v2.0
Tcta
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399108,180,157 - 108,183,174 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9108,180,157 - 108,183,359 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm389108,302,955 - 108,306,159 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,302,958 - 108,306,160 (-)Ensemblmm10GRCm38
MGSCv379108,205,289 - 108,208,282 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv369108,161,051 - 108,164,044 (-)NCBIMGSCv36mm8
Celera9107,912,001 - 107,914,995 (-)NCBICelera
Cytogenetic Map9F2NCBI
cM Map959.2NCBI
Tcta
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555321,347,639 - 1,349,864 (+)Ensembl
ChiLan1.0NW_0049555321,347,639 - 1,349,864 (+)NCBIChiLan1.0ChiLan1.0
TCTA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2249,394,560 - 49,398,654 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1349,399,352 - 49,403,426 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0349,340,010 - 49,344,288 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1350,584,614 - 50,588,891 (+)NCBIPanPan1.1PanPan1.1panPan2
TCTA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12039,820,845 - 39,824,526 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2039,822,211 - 39,824,200 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2039,739,296 - 39,742,977 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02040,177,073 - 40,180,753 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2040,177,073 - 40,180,399 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12039,544,617 - 39,548,297 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02039,948,238 - 39,951,919 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02040,227,822 - 40,231,502 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tcta
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560264,285,293 - 64,288,579 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365291,045,798 - 1,050,384 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365291,045,735 - 1,047,922 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TCTA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1331,991,610 - 31,998,129 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11331,991,408 - 31,995,274 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TCTA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12210,809,342 - 10,813,655 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2210,809,595 - 10,812,029 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666041156,200,733 - 156,205,008 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tcta
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247303,362,039 - 3,364,301 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247303,362,037 - 3,365,621 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tcta
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1899,630,696 - 99,633,931 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tcta
22 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:109
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000075241
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)8105462581132782436Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)882352698127352698Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)861019838121662124Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)849849908118871671Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)880768445125768445Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)880768445125768445Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)870041301121080908Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)868690349119799881Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)884192326129192326Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8103375781129871912Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102413464132782436Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)855428333127966348Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)884192326132782436Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)885348065130348065Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)879394435132782436Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)898145073122898010Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)880768445125768445Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)880768445125768445Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)891340911131690273Rat

Markers in Region
RH128269  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28108,988,695 - 108,988,905 (+)MAPPERmRatBN7.2
Rnor_6.08117,079,202 - 117,079,411NCBIRnor6.0
Rnor_5.08116,428,006 - 116,428,215UniSTSRnor5.0
Celera8108,291,718 - 108,291,927UniSTS
RH 3.4 Map81118.6UniSTS
Cytogenetic Map16q12.5UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000075241   ⟹   ENSRNOP00000067537
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl8117,867,153 - 117,871,331 (-)Ensembl
mRatBN7.2 Ensembl8108,988,590 - 108,991,564 (+)Ensembl
Rnor_6.0 Ensembl8117,079,095 - 117,082,162 (-)Ensembl
RefSeq Acc Id: NM_001014005   ⟹   NP_001014027
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,867,153 - 117,870,112 (-)NCBI
mRatBN7.28108,988,588 - 108,991,547 (-)NCBI
Rnor_6.08117,079,094 - 117,082,162 (-)NCBI
Rnor_5.08116,427,898 - 116,431,164 (-)NCBI
Celera8108,291,610 - 108,294,678 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001401234   ⟹   NP_001388163
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,867,153 - 117,870,112 (-)NCBI
mRatBN7.28108,988,588 - 108,991,547 (-)NCBI
RefSeq Acc Id: XM_008766514   ⟹   XP_008764736
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,867,153 - 117,871,132 (-)NCBI
mRatBN7.28108,988,588 - 108,992,321 (-)NCBI
Rnor_6.08117,079,094 - 117,082,338 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081326   ⟹   XP_038937254
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,867,153 - 117,871,132 (-)NCBI
mRatBN7.28108,988,588 - 108,992,324 (-)NCBI
RefSeq Acc Id: XM_039081327   ⟹   XP_038937255
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,867,153 - 117,871,132 (-)NCBI
mRatBN7.28108,988,588 - 108,992,323 (-)NCBI
RefSeq Acc Id: XM_039081328   ⟹   XP_038937256
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88117,867,153 - 117,871,132 (-)NCBI
mRatBN7.28108,988,588 - 108,992,314 (-)NCBI
RefSeq Acc Id: NP_001014027   ⟸   NM_001014005
- Peptide Label: isoform 2
- UniProtKB: Q5XIF1 (UniProtKB/Swiss-Prot),   A6I345 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764736   ⟸   XM_008766514
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000067537   ⟸   ENSRNOT00000075241
RefSeq Acc Id: XP_038937254   ⟸   XM_039081326
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937255   ⟸   XM_039081327
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038937256   ⟸   XM_039081328
- Peptide Label: isoform X4
RefSeq Acc Id: NP_001388163   ⟸   NM_001401234
- Peptide Label: isoform 1
- UniProtKB: A6I346 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIF1-F1-model_v2 AlphaFold Q5XIF1 1-106 view protein structure

Transcriptome

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

Promoters
RGD ID:13696295
Promoter ID:EPDNEW_R6819
Type:initiation region
Name:Tcta_1
Description:T-cell leukemia translocation altered
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08117,082,026 - 117,082,086EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359333 AgrOrtholog
BioCyc Gene G2FUF-29151 BioCyc
Ensembl Genes ENSRNOG00000048237 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000075241 ENTREZGENE
IMAGE_CLONE IMAGE:7191343 IMAGE-MGC_LOAD
InterPro TCTA UniProtKB/Swiss-Prot
KEGG Report rno:306587 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94634 IMAGE-MGC_LOAD
NCBI Gene 306587 ENTREZGENE
PANTHER PTHR32267 UniProtKB/Swiss-Prot
  T-CELL LEUKEMIA TRANSLOCATION-ALTERED GENE PROTEIN UniProtKB/Swiss-Prot
Pfam T_cell_tran_alt UniProtKB/Swiss-Prot
PhenoGen Tcta PhenoGen
PIRSF TCTA UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000048237 RatGTEx
RNAcentral URS00022B1EA1 RNACentral
UniProt A0ABK0M560_RAT UniProtKB/TrEMBL
  A6I344_RAT UniProtKB/TrEMBL
  A6I345 ENTREZGENE, UniProtKB/TrEMBL
  A6I346 ENTREZGENE, UniProtKB/TrEMBL
  Q5XIF1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-16 Tcta  T-cell leukemia translocation altered  Tcta  T-cell leukemia translocation altered gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Tcta  T-cell leukemia translocation altered gene  LOC306587  similar to RIKEN cDNA 9130410M22  Symbol and Name updated 1299863 APPROVED
2005-07-29 LOC306587  similar to RIKEN cDNA 9130410M22      Symbol and Name status set to provisional 70820 PROVISIONAL