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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28108,988,588 - 108,992,324 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,988,590 - 108,991,564 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8114,615,748 - 114,618,708 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08112,815,072 - 112,818,032 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08110,657,711 - 110,660,671 (-)NCBIRnor_WKY
Rnor_6.08117,079,094 - 117,082,338 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,079,095 - 117,082,162 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08116,427,898 - 116,431,164 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8108,291,610 - 108,294,678 (-)NCBICelera
Cytogenetic Map8q32NCBI
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
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
mRatBN7.28108,988,588 - 108,992,324 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8108,988,590 - 108,991,564 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8114,615,748 - 114,618,708 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.08112,815,072 - 112,818,032 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.08110,657,711 - 110,660,671 (-)NCBIRnor_WKY
Rnor_6.08117,079,094 - 117,082,338 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,079,095 - 117,082,162 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08116,427,898 - 116,431,164 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
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.p13 Ensembl349,412,212 - 49,416,476 (+)EnsemblGRCh38hg38GRCh38
GRCh37349,449,856 - 49,453,909 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36349,424,643 - 49,428,913 (+)NCBINCBI36Build 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
GRCm399108,180,154 - 108,183,358 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9108,180,157 - 108,183,359 (-)EnsemblGRCm39 Ensembl
GRCm389108,302,955 - 108,306,159 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,302,958 - 108,306,160 (-)EnsemblGRCm38mm10GRCm38
MGSCv379108,205,289 - 108,208,282 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555321,347,639 - 1,349,864 (+)NCBIChiLan1.0ChiLan1.0
TCTA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1350,584,614 - 50,588,891 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0349,340,010 - 49,344,288 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2039,739,296 - 39,742,977 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02040,177,073 - 40,180,753 (-)NCBIROS_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_1.0
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
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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247303,362,037 - 3,365,621 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tcta
7 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088624Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088624Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
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)873473045118473045Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2313400Anxrr25Anxiety related response QTL 25aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)889265192114019816Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat

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
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 43 55 39 19 39 8 11 74 35 41 11 8
Low 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075241   ⟹   ENSRNOP00000067537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
mRatBN7.28108,988,588 - 108,991,656 (-)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: XM_008766514   ⟹   XP_008764736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,988,588 - 108,992,324 (-)NCBI
RefSeq Acc Id: XM_039081327   ⟹   XP_038937255
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,988,588 - 108,992,323 (-)NCBI
RefSeq Acc Id: XM_039081328   ⟹   XP_038937256
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28108,988,588 - 108,992,314 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001014027   ⟸   NM_001014005
- UniProtKB: Q5XIF1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008764736   ⟸   XM_008766514
- Peptide Label: isoform X1
- Sequence:
RefSeq 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

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
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
Pfam T_cell_tran_alt UniProtKB/Swiss-Prot
PhenoGen Tcta PhenoGen
PIRSF TCTA UniProtKB/Swiss-Prot
UniProt 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