Tceanc (transcription elongation factor A N-terminal and central domain containing) - Rat Genome Database

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Gene: Tceanc (transcription elongation factor A N-terminal and central domain containing) Rattus norvegicus
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Symbol: Tceanc
Name: transcription elongation factor A N-terminal and central domain containing
RGD ID: 1584894
Description: Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human TCEANC (transcription elongation factor A N-terminal and central domain containing); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; chlormequat chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC367782; LOC367782; similar to transcription elongation factor A (SII), 3; transcription elongation factor A (SII) N-terminal and central domain containing; transcription elongation factor A N-terminal and central domain-containing protein
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
GRCr8X31,587,207 - 31,592,694 (+)NCBIGRCr8
mRatBN7.2X27,952,539 - 27,961,038 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX27,952,457 - 27,960,940 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX28,991,939 - 28,993,015 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X32,427,338 - 32,428,414 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X28,606,581 - 28,607,657 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X29,498,762 - 29,505,494 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX29,504,349 - 29,505,425 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X29,891,458 - 29,898,139 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,642,414 - 48,643,490 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX28,330,260 - 28,331,336 (+)NCBICelera
Cytogenetic MapXq13NCBI
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
nucleus  (IBA)

Molecular Function

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Tceanc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X31,587,207 - 31,592,694 (+)NCBIGRCr8
mRatBN7.2X27,952,539 - 27,961,038 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX27,952,457 - 27,960,940 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX28,991,939 - 28,993,015 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X32,427,338 - 32,428,414 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X28,606,581 - 28,607,657 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X29,498,762 - 29,505,494 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX29,504,349 - 29,505,425 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X29,891,458 - 29,898,139 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,642,414 - 48,643,490 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX28,330,260 - 28,331,336 (+)NCBICelera
Cytogenetic MapXq13NCBI
TCEANC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X13,653,141 - 13,665,409 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX13,653,112 - 13,681,964 (+)EnsemblGRCh38hg38GRCh38
GRCh37X13,671,260 - 13,683,528 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X13,581,228 - 13,592,168 (+)NCBINCBI36Build 36hg18NCBI36
CeleraX17,788,368 - 17,799,301 (+)NCBICelera
Cytogenetic MapXp22.2NCBI
HuRefX11,429,599 - 11,440,539 (+)NCBIHuRef
CHM1_1X13,702,140 - 13,713,079 (+)NCBICHM1_1
T2T-CHM13v2.0X13,234,528 - 13,246,800 (+)NCBIT2T-CHM13v2.0
Tceanc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X165,282,806 - 165,301,594 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX165,282,808 - 165,301,563 (-)EnsemblGRCm39 Ensembl
GRCm38X166,499,810 - 166,518,603 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX166,499,812 - 166,518,567 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X162,937,744 - 162,948,410 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X161,844,124 - 161,854,583 (-)NCBIMGSCv36mm8
CeleraX149,680,509 - 149,691,175 (-)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX77.59NCBI
Tceanc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555194,532,937 - 4,538,442 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555194,532,687 - 4,537,928 (-)NCBIChiLan1.0ChiLan1.0
TCEANC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X15,432,721 - 15,446,463 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X15,436,394 - 15,448,010 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X6,260,394 - 6,272,125 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X13,548,896 - 13,561,182 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX13,558,284 - 13,559,339 (+)Ensemblpanpan1.1panPan2
TCEANC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X10,070,367 - 10,079,532 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX10,078,451 - 10,079,503 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX10,044,842 - 10,054,032 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X10,028,216 - 10,037,411 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX10,036,330 - 10,037,382 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X10,097,025 - 10,106,240 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X10,088,180 - 10,097,395 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X10,114,339 - 10,123,557 (+)NCBIUU_Cfam_GSD_1.0
Tceanc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X3,223,012 - 3,235,212 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364703,231,900 - 3,232,958 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364703,225,387 - 3,233,034 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TCEANC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX10,293,684 - 10,312,431 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X10,293,676 - 10,305,033 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X11,247,421 - 11,258,772 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TCEANC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X12,143,433 - 12,158,973 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX12,157,872 - 12,158,924 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605613,963,012 - 13,975,095 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tceanc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624882482,345 - 483,406 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624882482,046 - 491,794 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tceanc
25 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000005981
Prediction methods:Miranda, Pita, 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
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2099094741052531Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2099094741203591Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000005981   ⟹   ENSRNOP00000005981
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX29,504,349 - 29,505,425 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000097777   ⟹   ENSRNOP00000086861
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX27,952,457 - 27,960,940 (+)Ensembl
RefSeq Acc Id: NM_001109015   ⟹   NP_001102485
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X31,589,313 - 31,590,389 (+)NCBI
mRatBN7.2X27,957,659 - 27,958,735 (+)NCBI
Rnor_6.0X29,504,349 - 29,505,425 (+)NCBI
Rnor_5.0X29,891,458 - 29,898,139 (+)NCBI
RGSC_v3.4X48,642,414 - 48,643,490 (+)RGD
CeleraX28,330,260 - 28,331,336 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256856   ⟹   XP_006256918
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X31,587,207 - 31,592,694 (+)NCBI
mRatBN7.2X27,952,539 - 27,961,038 (+)NCBI
Rnor_6.0X29,498,762 - 29,505,494 (+)NCBI
Rnor_5.0X29,891,458 - 29,898,139 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102485 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256918 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90556 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000086861.1
RefSeq Acc Id: NP_001102485   ⟸   NM_001109015
- UniProtKB: D4AEK4 (UniProtKB/TrEMBL),   A6K2H4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256918   ⟸   XM_006256856
- Peptide Label: isoform X1
- UniProtKB: D4AEK4 (UniProtKB/TrEMBL),   A6K2H4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000005981   ⟸   ENSRNOT00000005981
Ensembl Acc Id: ENSRNOP00000086861   ⟸   ENSRNOT00000097777
Protein Domains
TFIIS central   TFIIS N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEK4-F1-model_v2 AlphaFold D4AEK4 1-358 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584894 AgrOrtholog
BioCyc Gene G2FUF-2612 BioCyc
Ensembl Genes ENSRNOG00000004531 Ensembl
  ENSRNOG00000065918 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000097777.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.472.30 UniProtKB/TrEMBL
  1.20.930.10 UniProtKB/TrEMBL
  2.20.25.10 UniProtKB/TrEMBL
InterPro TF_IIS-typ UniProtKB/TrEMBL
  TFIIS/LEDGF_domain UniProtKB/TrEMBL
  TFIIS_cen_dom UniProtKB/TrEMBL
  TFIIS_cen_dom_sf UniProtKB/TrEMBL
  TFIIS_N UniProtKB/TrEMBL
KEGG Report rno:367782 UniProtKB/TrEMBL
NCBI Gene 367782 ENTREZGENE
PANTHER TRANSCRIPTION ELONGATION FACTOR A N-TERMINAL AND CENTRAL DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR S-II ZINC FINGER DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam TFIIS UniProtKB/TrEMBL
  TFIIS_M UniProtKB/TrEMBL
PhenoGen Tceanc PhenoGen
PIRSF TF_IIS UniProtKB/TrEMBL
PROSITE TFIIS_CENTRAL UniProtKB/TrEMBL
  TFIIS_N UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004531 RatGTEx
  ENSRNOG00000065918 RatGTEx
SMART TFS2M UniProtKB/TrEMBL
Superfamily-SCOP TFIIS_centre UniProtKB/TrEMBL
  TFIIS_conserved UniProtKB/TrEMBL
UniProt A6K2H4 ENTREZGENE, UniProtKB/TrEMBL
  D4AEK4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-19 Tceanc  transcription elongation factor A N-terminal and central domain containing  Tceanc  transcription elongation factor A (SII) N-terminal and central domain containing  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Tceanc  transcription elongation factor A (SII) N-terminal and central domain containing  LOC367782  similar to transcription elongation factor A (SII), 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-28 LOC367782  similar to transcription elongation factor A (SII), 3   LOC367782  similar to transcription elongation factor A (SII), 3 (predicted)  'predicted' is removed from gene name 2292626 APPROVED
2006-11-19 LOC367782  similar to transcription elongation factor A (SII), 3 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL