Tcea2 (transcription elongation factor A2) - Rat Genome Database

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Gene: Tcea2 (transcription elongation factor A2) Rattus norvegicus
Analyze
Symbol: Tcea2
Name: transcription elongation factor A2
RGD ID: 61825
Description: Predicted to enable DNA binding activity and zinc ion binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in centrosome and nucleoplasm. Predicted to be active in nucleus. Orthologous to human TCEA2 (transcription elongation factor A2); PARTICIPATES IN RNA polymerase II transcription elongation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: testis-specific S-II; transcription elongation factor A (SII) 2; transcription elongation factor A (SII), 2; transcription elongation factor A protein 2; transcription elongation factor S-II protein 2; transcription elongation factor TFIIS.l
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83189,173,756 - 189,181,633 (+)NCBIGRCr8
mRatBN7.23168,796,244 - 168,804,125 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,796,331 - 168,804,116 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,175,741 - 173,183,550 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,134,832 - 182,142,641 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,797,259 - 178,805,065 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,187,686 - 177,195,898 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,188,044 - 177,195,894 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,896,548 - 180,904,402 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,831,286 - 170,839,091 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,737,321 - 170,745,127 (+)NCBI
Celera3163,783,634 - 163,791,446 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centrosome  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA)

Molecular Function

Molecular Pathway 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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Control of transcriptional elongation. Kwak H and Lis JT, Annu Rev Genet. 2013;47:483-508. doi: 10.1146/annurev-genet-110711-155440. Epub 2013 Sep 11.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. Cloning and identification of testis-specific transcription elongation factor S-II. Xu Q, etal., J Biol Chem 1994 Jan 28;269(4):3100-3.

Genomics

Comparative Map Data
Tcea2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83189,173,756 - 189,181,633 (+)NCBIGRCr8
mRatBN7.23168,796,244 - 168,804,125 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,796,331 - 168,804,116 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,175,741 - 173,183,550 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,134,832 - 182,142,641 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,797,259 - 178,805,065 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,187,686 - 177,195,898 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,188,044 - 177,195,894 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,896,548 - 180,904,402 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,831,286 - 170,839,091 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,737,321 - 170,745,127 (+)NCBI
Celera3163,783,634 - 163,791,446 (-)NCBICelera
Cytogenetic Map3q43NCBI
TCEA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382064,055,596 - 64,072,347 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2064,049,836 - 64,072,347 (+)EnsemblGRCh38hg38GRCh38
GRCh372062,688,325 - 62,703,700 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362062,158,883 - 62,174,143 (+)NCBINCBI36Build 36hg18NCBI36
Build 342062,158,882 - 62,174,144NCBI
Celera2059,374,545 - 59,389,785 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2059,422,225 - 59,437,466 (+)NCBIHuRef
CHM1_12062,589,462 - 62,604,716 (+)NCBICHM1_1
T2T-CHM13v2.02065,875,622 - 65,892,426 (+)NCBIT2T-CHM13v2.0
Tcea2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392181,322,090 - 181,329,860 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2181,322,103 - 181,329,864 (+)EnsemblGRCm39 Ensembl
GRCm382181,680,297 - 181,688,067 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,680,310 - 181,688,071 (+)EnsemblGRCm38mm10GRCm38
MGSCv372181,415,015 - 181,422,756 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362181,609,716 - 181,617,457 (+)NCBIMGSCv36mm8
Celera2185,762,702 - 185,770,433 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.72NCBI
Tcea2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955528186,642 - 194,058 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955528186,642 - 194,058 (-)NCBIChiLan1.0ChiLan1.0
TCEA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22169,880,980 - 69,890,213 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12069,873,001 - 69,882,229 (+)NCBINHGRI_mPanPan1
PanPan1.12061,977,338 - 61,986,592 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2061,976,869 - 61,986,592 (+)Ensemblpanpan1.1panPan2
TCEA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,508,161 - 47,512,399 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,508,136 - 47,537,250 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,639,396 - 46,646,271 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02448,644,476 - 48,651,329 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12447,489,097 - 47,495,956 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,613,543 - 47,620,400 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02448,352,514 - 48,359,386 (+)NCBIUU_Cfam_GSD_1.0
Tcea2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,789,352 - 195,796,792 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651411,242,739 - 11,250,260 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651411,243,021 - 11,251,216 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TCEA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,866,377 - 62,888,787 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,866,594 - 62,888,790 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TCEA2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12174,158 - 184,237 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2174,134 - 182,943 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605047,607,379 - 47,629,161 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tcea2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,692,006 - 29,699,383 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474129,691,983 - 29,699,383 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tcea2
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:112
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000022073
Prediction methods:Microtar, 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
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)343827364169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
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)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat


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 2 2 2 2 74 18 38
Low 3 41 52 36 17 36 8 11 17 3 11 8
Below cutoff 3 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022073   ⟹   ENSRNOP00000022073
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,796,331 - 168,804,116 (+)Ensembl
Rnor_6.0 Ensembl3177,188,044 - 177,195,894 (+)Ensembl
RefSeq Acc Id: NM_057098   ⟹   NP_476439
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,173,826 - 189,181,632 (+)NCBI
mRatBN7.23168,796,317 - 168,804,123 (+)NCBI
Rnor_6.03177,188,063 - 177,195,870 (+)NCBI
Rnor_5.03180,896,548 - 180,904,402 (+)NCBI
RGSC_v3.43170,831,286 - 170,839,091 (+)RGD
Celera3163,783,634 - 163,791,446 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235740   ⟹   XP_006235802
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,173,767 - 189,181,633 (+)NCBI
mRatBN7.23168,796,256 - 168,804,125 (+)NCBI
Rnor_6.03177,188,013 - 177,195,898 (+)NCBI
Rnor_5.03180,896,548 - 180,904,402 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235741   ⟹   XP_006235803
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,173,773 - 189,181,633 (+)NCBI
mRatBN7.23168,796,275 - 168,804,125 (+)NCBI
Rnor_6.03177,188,014 - 177,195,898 (+)NCBI
Rnor_5.03180,896,548 - 180,904,402 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235742   ⟹   XP_006235804
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,173,756 - 189,181,633 (+)NCBI
mRatBN7.23168,796,244 - 168,804,125 (+)NCBI
Rnor_6.03177,188,014 - 177,195,898 (+)NCBI
Rnor_5.03180,896,548 - 180,904,402 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_476439   ⟸   NM_057098
- UniProtKB: Q63799 (UniProtKB/Swiss-Prot),   A0A8L2QBN2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235804   ⟸   XM_006235742
- Peptide Label: isoform X3
- UniProtKB: A0A8L2QBN2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235802   ⟸   XM_006235740
- Peptide Label: isoform X1
- UniProtKB: A0A8L2QBN2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235803   ⟸   XM_006235741
- Peptide Label: isoform X2
- UniProtKB: A0A8L2QBN2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022073   ⟸   ENSRNOT00000022073
Protein Domains
TFIIS central   TFIIS N-terminal   TFIIS-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63799-F1-model_v2 AlphaFold Q63799 1-299 view protein structure

Transcriptome

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

Promoters
RGD ID:13692764
Promoter ID:EPDNEW_R3287
Type:initiation region
Name:Tcea2_1
Description:transcription elongation factor A2
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_6.03177,188,033 - 177,188,093EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61825 AgrOrtholog
BioCyc Gene G2FUF-46263 BioCyc
Ensembl Genes ENSRNOG00000016288 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022073.8 UniProtKB/TrEMBL
Gene3D-CATH 1.10.472.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.930.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.20.25.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro TF_IIS-typ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS/CRSP70_N_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS/LEDGF_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_cen_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_cen_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFSII UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_TFIIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29575 UniProtKB/Swiss-Prot
NCBI Gene 29575 ENTREZGENE
PANTHER TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR S-II ZINC FINGER DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Med26 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tcea2 PhenoGen
PIRSF TF_IIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TFIIS_CENTRAL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_TFIIS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_TFIIS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016288 RatGTEx
SMART TFS2M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFS2N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C2C2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46942 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47676 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zinc beta-ribbon UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QBN2 ENTREZGENE, UniProtKB/TrEMBL
  A6KLY3_RAT UniProtKB/TrEMBL
  Q63799 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-19 Tcea2  transcription elongation factor A2  Tcea2  transcription elongation factor A (SII), 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Tcea2  transcription elongation factor A (SII), 2    transcription elongation factor A2  Name updated 1299863 APPROVED
2002-06-10 Tcea2  transcription elongation factor A2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA expressed specifically in testis 619610
gene_protein predicted protein contains 299 aa residues 619610