Human Gene TCEB1 (uc022avx.1) Description and Page Index
  Description: Homo sapiens transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) (TCEB1), transcript variant 3, mRNA.
RefSeq Summary (NM_001204858): This gene encodes the protein elongin C, which is a subunit of the transcription factor B (SIII) complex. The SIII complex is composed of elongins A/A2, B and C. It activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin A functions as the transcriptionally active component of the SIII complex, whereas elongins B and C are regulatory subunits. Elongin A2 is specifically expressed in the testis, and capable of forming a stable complex with elongins B and C. The von Hippel-Lindau tumor suppressor protein binds to elongins B and C, and thereby inhibits transcription elongation. Multiple alternatively spliced transcript variants encoding two distinct isoforms have been identified. [provided by RefSeq, Mar 2011].
Transcript (Including UTRs)
   Position: hg19 chr8:74,857,373-74,884,522 Size: 27,150 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr8:74,858,865-74,872,003 Size: 13,139 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:74,857,373-74,884,522)mRNA (may differ from genome)Protein (112 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ELOC_HUMAN
DESCRIPTION: RecName: Full=Transcription elongation factor B polypeptide 1; AltName: Full=Elongin 15 kDa subunit; AltName: Full=Elongin-C; Short=EloC; AltName: Full=RNA polymerase II transcription factor SIII subunit C; AltName: Full=SIII p15;
FUNCTION: SIII, also known as elongin, is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. Subunit A is transcriptionally active and its transcription activity is strongly enhanced by binding to the dimeric complex of the SIII regulatory subunits B and C (elongin BC complex).
FUNCTION: The elongin BC complex seems to be involved as an adapter protein in the proteasomal degradation of target proteins via different E3 ubiquitin ligase complexes, including the von Hippel-Lindau ubiquitination complex CBC(VHL). By binding to BC- box motifs it seems to link target recruitment subunits, like VHL and members of the SOCS box family, to Cullin/RBX1 modules that activate E2 ubiquitination enzymes.
SUBUNIT: Heterotrimer of an A (A1, A2 or A3), B and C subunit. Part of E3 ubiquitin ligase complexes with CUL5 or CUL2, RBX1 and a substrate adapter protein that can be either SOCS1, SOCS5, TCEB3, VHL or WSB1 (By similarity). The elongin BC complex is part of a complex with hydroxylated HIF1A. Substrate adapter protein can be a viral protein such as HIV Vif. Interacts with VHL. Interacts with TMF1. Interacts with human respiratory syncytial virus (HRSV) protein NS1.
INTERACTION: Q96G25:MED8; NbExp=3; IntAct=EBI-301231, EBI-394405; Q99619:SPSB2; NbExp=3; IntAct=EBI-301231, EBI-2323209; Q96A44:SPSB4; NbExp=2; IntAct=EBI-301231, EBI-2323233; Q15370:TCEB2; NbExp=3; IntAct=EBI-301231, EBI-301238; P12504:vif (xeno); NbExp=5; IntAct=EBI-301231, EBI-779991;
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Overexpressed in prostate cancer cell line PC- 3 and breast cancer cell line SK-BR-3.
SIMILARITY: Belongs to the SKP1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TCEB1
CDC HuGE Published Literature: TCEB1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.62 RPKM in Testis
Total median expression: 393.80 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -161.70404-0.400 Picture PostScript Text
3' UTR -387.181492-0.260 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011333 - BTB/POZ_fold
IPR001232 - Skp1_comp
IPR016073 - Skp1_comp_POZ

Pfam Domains:
PF03931 - Skp1 family, tetramerisation domain

SCOP Domains:
54695 - POZ domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1LM8
- X-ray MuPIT

1LQB
- X-ray MuPIT

1VCB
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2C9W - X-ray MuPIT 2IZV - X-ray MuPIT 2XAI - X-ray
3DCG - X-ray MuPIT 3ZRC - X-ray 3ZRF - X-ray
3ZTC - X-ray MuPIT 3ZTD - X-ray MuPIT 3ZUN - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15369
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0004842 ubiquitin-protein transferase activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016032 viral process
GO:0016567 protein ubiquitination
GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter
GO:0043687 post-translational protein modification
GO:0061418 regulation of transcription from RNA polymerase II promoter in response to hypoxia

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0070449 elongin complex


-  Descriptions from all associated GenBank mRNAs
  AK057889 - Homo sapiens cDNA FLJ25160 fis, clone CBR08077, highly similar to Rat elongation factor SIII p15 subunit mRNA.
LF383592 - JP 2014500723-A/191095: Polycomb-Associated Non-Coding RNAs.
AL832244 - Homo sapiens mRNA; cDNA DKFZp686L1077 (from clone DKFZp686L1077).
JD446717 - Sequence 427741 from Patent EP1572962.
JD408223 - Sequence 389247 from Patent EP1572962.
JD481885 - Sequence 462909 from Patent EP1572962.
JD125782 - Sequence 106806 from Patent EP1572962.
JD152447 - Sequence 133471 from Patent EP1572962.
JD408224 - Sequence 389248 from Patent EP1572962.
JD481884 - Sequence 462908 from Patent EP1572962.
JD481886 - Sequence 462910 from Patent EP1572962.
JD277359 - Sequence 258383 from Patent EP1572962.
JD401803 - Sequence 382827 from Patent EP1572962.
JD325463 - Sequence 306487 from Patent EP1572962.
JD393316 - Sequence 374340 from Patent EP1572962.
JD055861 - Sequence 36885 from Patent EP1572962.
JD439864 - Sequence 420888 from Patent EP1572962.
JD249822 - Sequence 230846 from Patent EP1572962.
JD148291 - Sequence 129315 from Patent EP1572962.
JD463804 - Sequence 444828 from Patent EP1572962.
LF317114 - JP 2014500723-A/124617: Polycomb-Associated Non-Coding RNAs.
BX649138 - Homo sapiens mRNA; cDNA DKFZp686J19157 (from clone DKFZp686J19157).
BC100283 - Homo sapiens transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C), mRNA (cDNA clone MGC:117336 IMAGE:6061521), complete cds.
BC013809 - Homo sapiens transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C), mRNA (cDNA clone MGC:8963 IMAGE:3923736), complete cds.
BC093065 - Homo sapiens transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C), mRNA (cDNA clone MGC:111173 IMAGE:30411791), complete cds.
L34587 - Homo sapiens RNA polymerase II elongation factor SIII, p15 subunit mRNA, complete cds.
EU176247 - Synthetic construct Homo sapiens clone IMAGE:100006361; FLH168553.01X; RZPDo839E08250D transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) (TCEB1) gene, encodes complete protein.
DQ894197 - Synthetic construct Homo sapiens clone IMAGE:100008657; FLH168548.01L; RZPDo839A0893D transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) (TCEB1) gene, encodes complete protein.
AB464300 - Synthetic construct DNA, clone: pF1KB7509, Homo sapiens TCEB1 gene for transcription elongation factor B (SIII), polypeptide 1, without stop codon, in Flexi system.
LF317115 - JP 2014500723-A/124618: Polycomb-Associated Non-Coding RNAs.
LF317116 - JP 2014500723-A/124619: Polycomb-Associated Non-Coding RNAs.
LF317117 - JP 2014500723-A/124620: Polycomb-Associated Non-Coding RNAs.
MA619169 - JP 2018138019-A/191095: Polycomb-Associated Non-Coding RNAs.
MA552691 - JP 2018138019-A/124617: Polycomb-Associated Non-Coding RNAs.
MA552692 - JP 2018138019-A/124618: Polycomb-Associated Non-Coding RNAs.
MA552693 - JP 2018138019-A/124619: Polycomb-Associated Non-Coding RNAs.
MA552694 - JP 2018138019-A/124620: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04120 - Ubiquitin mediated proteolysis
hsa05200 - Pathways in cancer
hsa05211 - Renal cell carcinoma

Reactome (by CSHL, EBI, and GO)

Protein Q15369 (Reactome details) participates in the following event(s):

R-HSA-112435 Formation of Elongin BC complex
R-HSA-112436 Formation of Elongin complex
R-HSA-180555 Association of APOBEC3G:Vif with the Cul5-SCF complex
R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-167077 Recruitment of elongation factors to form HIV-1 elongation complex
R-HSA-167196 Recruitment of elongation factors to form HIV-1 elongation complex
R-HSA-113429 Elongating transcript encounters a lesion in the template
R-HSA-1234169 Nuclear VHL:EloB,C:CUL2:RBX1 binds hydroxyprolyl-HIF-alpha
R-HSA-180540 Multi-ubiquitination of APOBEC3G
R-HSA-8956099 VHL:EloB,C:NEDD8-CUL2:RBX1 complex binds UBXN7
R-HSA-8956103 VHL:EloB,C:NEDD8-CUL2:RBX1 complex binds hydroxyprolyl-HIF-alpha
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-8955241 CAND1 binds cytosolic CRL E3 ubiquitin ligases
R-HSA-8952039 NEDD8:AcM-UBE2F binds CRL5 E3 ubiquitin ligase complex
R-HSA-8952044 AcM-UBE2F transfers NEDD8 to CRL5 E3 ubiquitin ligase complex
R-HSA-112385 Addition of nucleotides leads to transcript elongation
R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing
R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates
R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest
R-HSA-112392 Resumption of elongation after recovery from pausing
R-HSA-113413 TFIIS-mediated recovery of elongation from arrest
R-HSA-112395 Abortive termination of elongation after arrest
R-HSA-112396 Separation of elongating transcript from template
R-HSA-167150 Resumption of elongation of HIV-1 transcript after recovery from pausing
R-HSA-167076 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing
R-HSA-167282 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing
R-HSA-167284 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest
R-HSA-167288 TFIIS-mediated recovery of HIV-1 elongation from arrest
R-HSA-167292 Resumption of elongation of HIV-1 transcript after recovery from pausing
R-HSA-167148 TFIIS-mediated recovery of elongation from arrest
R-HSA-167459 Abortive termination of HIV-1 elongation after arrest (Tat-containing elongation complex)
R-HSA-167090 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest
R-HSA-167192 Pol II elongation complex moves on the HIV-1 template as transcript elongates
R-HSA-167181 Addition of nucleotides leads to HIV-1 transcript elongation
R-HSA-167197 Separation of elongating HIV-1 transcript from template
R-HSA-167481 Abortive termination of HIV-1 elongation after arrest
R-HSA-6797616 CCNK:CDK12 binds RNA Pol II at DNA repair genes
R-HSA-1234172 Nuclear VBC complex ubiquitinylates HIF-alpha
R-HSA-1234183 Cytosolic VHL:EloB,C:CUL2:RBX1 binds hydroxyprolyl-HIF-alpha
R-HSA-8956106 VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-8955289 COMMDs displace CAND1 from cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-8956040 COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-6797606 CDK12 phosphorylates RNA Pol II CTD at DNA repair genes
R-HSA-1234163 Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha
R-HSA-1234173 Cytosolic PHD2,3 hydroxylates proline residues on HIF3A
R-HSA-1234177 Cytosolic PHD2,3 hydroxylates proline residues on HIF1A
R-HSA-1234179 Cytosolic PHD2,3 hydroxylates proline residues on EPAS1 (HIF2A)
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-180585 Vif-mediated degradation of APOBEC3G
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-74160 Gene expression (Transcription)
R-HSA-162909 Host Interactions of HIV factors
R-HSA-8951664 Neddylation
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-376176 Signaling by ROBO receptors
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-167238 Pausing and recovery of Tat-mediated HIV elongation
R-HSA-167290 Pausing and recovery of HIV elongation
R-HSA-167287 HIV elongation arrest and recovery
R-HSA-167243 Tat-mediated HIV elongation arrest and recovery
R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript
R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-HSA-167172 Transcription of the HIV genome
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-162906 HIV Infection
R-HSA-597592 Post-translational protein modification
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-422475 Axon guidance
R-HSA-167169 HIV Transcription Elongation
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-2262749 Cellular response to hypoxia
R-HSA-5663205 Infectious disease
R-HSA-392499 Metabolism of proteins
R-HSA-1280218 Adaptive Immune System
R-HSA-1266738 Developmental Biology
R-HSA-212436 Generic Transcription Pathway
R-HSA-162587 HIV Life Cycle
R-HSA-2262752 Cellular responses to stress
R-HSA-1643685 Disease
R-HSA-168256 Immune System
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: ELOC_HUMAN, NM_001204858, NP_001191793, Q15369, Q567Q6
UCSC ID: uc022avx.1
RefSeq Accession: NM_001204858
Protein: Q15369 (aka ELOC_HUMAN)
CCDS: CCDS34910.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001204858.1
exon count: 5CDS single in 3' UTR: no RNA size: 2235
ORF size: 339CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 878.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.