Tcea1 (transcription elongation factor A1) - Rat Genome Database

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Gene: Tcea1 (transcription elongation factor A1) Rattus norvegicus
Analyze
Symbol: Tcea1
Name: transcription elongation factor A1
RGD ID: 1309880
Description: Predicted to enable DNA binding activity and zinc ion binding activity. Involved in positive regulation of exoribonuclease activity. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of transcription factor TFIID complex. Predicted to be active in nucleus. Orthologous to human TCEA1 (transcription elongation factor A1); PARTICIPATES IN RNA polymerase II transcription elongation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362479; MGC116288; transcription elongation factor A (SII) 1; transcription elongation factor A protein 1; transcription elongation factor S-II protein 1
RGD Orthologs
Human
Mouse
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Tcea1l1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2514,631,454 - 14,668,769 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl514,631,454 - 14,668,745 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx516,825,171 - 16,862,994 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01513,439,353 - 13,441,754 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0518,159,843 - 18,197,667 (-)NCBIRnor_WKY
Rnor_6.0514,511,183 - 14,548,494 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl514,511,183 - 14,548,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0519,293,482 - 19,330,800 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4514,834,045 - 14,871,291 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1514,834,044 - 14,871,291 (-)NCBI
Celera514,002,673 - 14,039,908 (-)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Comparative TFIIS-mediated transcript cleavage by mammalian RNA polymerase II arrested at a lesion in different transcription systems. Kalogeraki VS, etal., DNA Repair (Amst). 2005 Sep 28;4(10):1075-87.
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. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:12761297   PMID:12943681   PMID:15489334   PMID:16581793   PMID:16854843   PMID:27193682  


Genomics

Comparative Map Data
Tcea1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2514,631,454 - 14,668,769 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl514,631,454 - 14,668,745 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx516,825,171 - 16,862,994 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01513,439,353 - 13,441,754 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0518,159,843 - 18,197,667 (-)NCBIRnor_WKY
Rnor_6.0514,511,183 - 14,548,494 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl514,511,183 - 14,548,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0519,293,482 - 19,330,800 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4514,834,045 - 14,871,291 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1514,834,044 - 14,871,291 (-)NCBI
Celera514,002,673 - 14,039,908 (-)NCBICelera
Cytogenetic Map5q12NCBI
TCEA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38853,966,556 - 54,022,448 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl853,966,552 - 54,022,456 (-)EnsemblGRCh38hg38GRCh38
GRCh37854,879,116 - 54,935,008 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36855,041,669 - 55,097,561 (-)NCBINCBI36Build 36hg18NCBI36
Celera850,869,815 - 50,924,590 (-)NCBICelera
Cytogenetic Map8q11.23NCBI
HuRef850,347,344 - 50,402,986 (-)NCBIHuRef
CHM1_1854,930,631 - 54,986,634 (-)NCBICHM1_1
T2T-CHM13v2.0854,343,951 - 54,399,849 (-)NCBIT2T-CHM13v2.0
Tcea1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914,927,917 - 4,968,132 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14,928,037 - 4,968,132 (+)EnsemblGRCm39 Ensembl
GRCm3814,857,694 - 4,897,909 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14,857,814 - 4,897,909 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714,847,775 - 4,887,990 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614,847,896 - 4,887,986 (+)NCBIMGSCv36mm8
Celera14,869,075 - 4,909,317 (+)NCBICelera
Cytogenetic Map1A1NCBI
TCEA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl477,109,594 - 77,138,320 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1477,109,555 - 77,138,324 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2484,179,838 - 84,208,587 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TCEA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1850,048,771 - 50,104,189 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl850,048,474 - 50,104,130 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603991,833,826 - 91,890,759 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tcea1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247351,637,465 - 1,704,154 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247351,637,453 - 1,700,839 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tcea1
146 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:436
Count of miRNA genes:243
Interacting mature miRNAs:279
Transcripts:ENSRNOT00000010893
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat

Markers in Region
RH140518  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21510,403,143 - 10,403,336 (+)MAPPERmRatBN7.2
mRatBN7.2514,631,582 - 14,631,725 (+)MAPPERmRatBN7.2
Rnor_6.0514,511,312 - 14,511,454NCBIRnor6.0
Rnor_6.01511,652,013 - 11,652,205NCBIRnor6.0
Rnor_5.01515,690,726 - 15,690,918UniSTSRnor5.0
Rnor_5.0519,293,611 - 19,293,753UniSTSRnor5.0
RGSC_v3.4514,834,174 - 14,834,316UniSTSRGSC3.4
RGSC_v3.41511,881,548 - 11,881,740UniSTSRGSC3.4
Celera1510,413,518 - 10,413,710UniSTS
Celera514,002,802 - 14,002,944UniSTS
Cytogenetic Map5q12UniSTS
Cytogenetic Map15p16UniSTS
RH140111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2514,648,621 - 14,648,824 (+)MAPPERmRatBN7.2
Rnor_6.0514,528,350 - 14,528,552NCBIRnor6.0
Rnor_5.0519,310,650 - 19,310,852UniSTSRnor5.0
RGSC_v3.4514,851,212 - 14,851,414UniSTSRGSC3.4
Celera514,019,841 - 14,020,043UniSTS
Cytogenetic Map5q12UniSTS
RH141473  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21510,402,454 - 10,402,604 (+)MAPPERmRatBN7.2
mRatBN7.2514,632,264 - 14,632,414 (-)MAPPERmRatBN7.2
mRatBN7.2514,632,264 - 14,632,414 (+)MAPPERmRatBN7.2
mRatBN7.21510,402,454 - 10,402,604 (-)MAPPERmRatBN7.2
Rnor_6.01511,651,324 - 11,651,473NCBIRnor6.0
Rnor_6.0514,511,994 - 14,512,143NCBIRnor6.0
Rnor_5.0519,294,293 - 19,294,442UniSTSRnor5.0
Rnor_5.01515,690,037 - 15,690,186UniSTSRnor5.0
RGSC_v3.4514,834,856 - 14,835,005UniSTSRGSC3.4
RGSC_v3.41511,880,859 - 11,881,008UniSTSRGSC3.4
Celera1510,412,829 - 10,412,978UniSTS
Celera514,003,484 - 14,003,633UniSTS
Cytogenetic Map15p16UniSTS
Cytogenetic Map5q12UniSTS


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 57 41 19 41 8 10 74 35 41 11 8
Low 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010893   ⟹   ENSRNOP00000010893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl514,631,457 - 14,668,745 (-)Ensembl
Rnor_6.0 Ensembl514,511,183 - 14,548,429 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104892   ⟹   ENSRNOP00000084958
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl514,631,454 - 14,668,703 (-)Ensembl
RefSeq Acc Id: NM_001025735   ⟹   NP_001020906
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2514,631,454 - 14,668,704 (-)NCBI
Rnor_6.0514,511,183 - 14,548,429 (-)NCBI
Rnor_5.0519,293,482 - 19,330,800 (-)NCBI
RGSC_v3.4514,834,045 - 14,871,291 (-)RGD
Celera514,002,673 - 14,039,908 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237816   ⟹   XP_006237878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2514,631,454 - 14,668,769 (-)NCBI
Rnor_6.0514,511,183 - 14,548,494 (-)NCBI
Rnor_5.0519,293,482 - 19,330,800 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110212   ⟹   XP_038966140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2514,631,454 - 14,668,212 (-)NCBI
RefSeq Acc Id: XM_039110213   ⟹   XP_038966141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2514,631,454 - 14,668,215 (-)NCBI
RefSeq Acc Id: XM_039110214   ⟹   XP_038966142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2514,631,454 - 14,662,619 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020906   ⟸   NM_001025735
- UniProtKB: Q4KLL0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237878   ⟸   XM_006237816
- Peptide Label: isoform X1
- UniProtKB: Q4KLL0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010893   ⟸   ENSRNOT00000010893
RefSeq Acc Id: XP_038966141   ⟸   XM_039110213
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966140   ⟸   XM_039110212
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966142   ⟸   XM_039110214
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000084958   ⟸   ENSRNOT00000104892
Protein Domains
TFIIS central   TFIIS N-terminal   TFIIS-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4KLL0-F1-model_v2 AlphaFold Q4KLL0 1-301 view protein structure

Transcriptome

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

Promoters
RGD ID:13693542
Promoter ID:EPDNEW_R4067
Type:multiple initiation site
Name:LOC498453_1
Description:similar to transcription elongation factor A 1 isoform 2
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_6.0514,548,468 - 14,548,528EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309880 AgrOrtholog
BioCyc Gene G2FUF-42153 BioCyc
Ensembl Genes ENSRNOG00000005869 UniProtKB/Swiss-Prot
  ENSRNOG00000022323 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010893.6 UniProtKB/TrEMBL
  ENSRNOP00000084958 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000097722 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007696 UniProtKB/Swiss-Prot
  ENSRNOT00000010893.7 UniProtKB/TrEMBL
  ENSRNOT00000104892 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.472.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.930.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7460791 IMAGE-MGC_LOAD
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:362479 UniProtKB/Swiss-Prot
  rno:498453 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116288 IMAGE-MGC_LOAD
NCBI Gene 362479 ENTREZGENE
Pfam Med26 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS_M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tcea1 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
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
TIGRFAMs TFSII UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2Q4Y0_RAT UniProtKB/TrEMBL
  Q4KLL0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-19 Tcea1  transcription elongation factor A1  Tcea1  transcription elongation factor A (SII) 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tcea1  transcription elongation factor A (SII) 1  Tcea1_predicted  transcription elongation factor A (SII) 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tcea1_predicted  transcription elongation factor A (SII) 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED