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 have DNA binding activity and zinc ion binding activity. Involved in positive regulation of exoribonuclease activity. Predicted to localize to nucleolus and transcription factor TFIID complex. Orthologous to human TCEA1 (transcription elongation factor A1); PARTICIPATES IN RNA polymerase II transcription elongation pathway; INTERACTS WITH 17alpha-ethynylestradiol; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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 ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2514,631,454 - 14,668,769 (-)NCBI
Rnor_6.0 Ensembl514,511,183 - 14,548,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0514,511,183 - 14,548,494 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0519,293,482 - 19,330,800 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4514,834,045 - 14,871,291 (-)NCBIRGSC3.4rn4RGSC3.4
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

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 (-)NCBI
Rnor_6.0 Ensembl514,511,183 - 14,548,429 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0514,511,183 - 14,548,494 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0519,293,482 - 19,330,800 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4514,834,045 - 14,871,291 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl853,966,552 - 54,022,456 (-)EnsemblGRCh38hg38GRCh38
GRCh38853,966,556 - 54,022,448 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37854,879,116 - 54,935,008 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36855,041,669 - 55,097,561 (-)NCBINCBI36hg18NCBI36
Celera850,869,815 - 50,924,590 (-)NCBI
Cytogenetic Map8q11.23NCBI
HuRef850,347,344 - 50,402,986 (-)NCBIHuRef
CHM1_1854,930,629 - 54,986,642 (-)NCBICHM1_1
Tcea1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914,927,917 - 4,968,132 (+)NCBIGRCm39mm39
GRCm39 Ensembl14,928,037 - 4,968,132 (+)Ensembl
GRCm3814,857,694 - 4,897,909 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14,857,814 - 4,897,909 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714,847,775 - 4,887,990 (+)NCBIGRCm37mm9NCBIm37
MGSCv3614,847,896 - 4,887,986 (+)NCBImm8
Celera14,869,075 - 4,909,317 (+)NCBICelera
Cytogenetic Map1A1NCBI
TCEA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl477,109,507 - 77,138,362 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1850,048,771 - 50,104,189 (-)NCBI
ChlSab1.1 Ensembl850,048,474 - 50,104,130 (-)Ensembl
Tcea1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247351,637,453 - 1,700,839 (+)NCBI

Position Markers
RH140518  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01511,652,013 - 11,652,205NCBIRnor6.0
Rnor_6.0514,511,312 - 14,511,454NCBIRnor6.0
Rnor_5.01515,690,726 - 15,690,918UniSTSRnor5.0
Rnor_5.0519,293,611 - 19,293,753UniSTSRnor5.0
RGSC_v3.41511,881,548 - 11,881,740UniSTSRGSC3.4
RGSC_v3.4514,834,174 - 14,834,316UniSTSRGSC3.4
Celera1510,413,518 - 10,413,710UniSTS
Celera514,002,802 - 14,002,944UniSTS
Cytogenetic Map5q12UniSTS
Cytogenetic Map15p16UniSTS
RH140111  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Rnor_6.01511,651,324 - 11,651,473NCBIRnor6.0
Rnor_6.0514,511,994 - 14,512,143NCBIRnor6.0
Rnor_5.01515,690,037 - 15,690,186UniSTSRnor5.0
Rnor_5.0519,294,293 - 19,294,442UniSTSRnor5.0
RGSC_v3.41511,880,859 - 11,881,008UniSTSRGSC3.4
RGSC_v3.4514,834,856 - 14,835,005UniSTSRGSC3.4
Celera1510,412,829 - 10,412,978UniSTS
Celera514,003,484 - 14,003,633UniSTS
Cytogenetic Map15p16UniSTS
Cytogenetic Map5q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
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)5166658771552720Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5787561118592319Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51328888858288888Rat

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.


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
Rnor_6.0 Ensembl514,511,183 - 14,548,429 (-)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
Protein Domains
TFIIS central   TFIIS N-terminal

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309880 AgrOrtholog
Ensembl Genes ENSRNOG00000022323 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000010893 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010893 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.472.30 UniProtKB/Swiss-Prot
  1.20.930.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7460791 IMAGE-MGC_LOAD
InterPro TF_IIS-typ UniProtKB/Swiss-Prot
  TFIIS/CRSP70_N_sub UniProtKB/Swiss-Prot
  TFIIS/LEDGF_dom_sf UniProtKB/Swiss-Prot
  TFIIS_cen_dom UniProtKB/Swiss-Prot
  TFIIS_cen_dom_sf UniProtKB/Swiss-Prot
  TFIIS_N UniProtKB/Swiss-Prot
  TFSII UniProtKB/Swiss-Prot
  Znf_TFIIS UniProtKB/Swiss-Prot
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
  TFIIS_C UniProtKB/Swiss-Prot
  TFIIS_M UniProtKB/Swiss-Prot
PhenoGen Tcea1 PhenoGen
PIRSF TF_IIS UniProtKB/Swiss-Prot
PROSITE TFIIS_CENTRAL UniProtKB/Swiss-Prot
  TFIIS_N UniProtKB/Swiss-Prot
  ZF_TFIIS_1 UniProtKB/Swiss-Prot
  ZF_TFIIS_2 UniProtKB/Swiss-Prot
SMART TFS2M UniProtKB/Swiss-Prot
  TFS2N UniProtKB/Swiss-Prot
  ZnF_C2C2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46942 UniProtKB/Swiss-Prot
  SSF47676 UniProtKB/Swiss-Prot
TIGRFAMs TFSII UniProtKB/Swiss-Prot
UniProt 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