Human Gene THOC6 (uc002ctb.2) Description and Page Index
  Description: Homo sapiens THO complex 6 homolog (Drosophila) (THOC6), transcript variant 1, mRNA.
RefSeq Summary (NM_024339): This gene encodes a subunit of the multi-protein THO complex, which is involved in coordination between transcription and mRNA processing. The THO complex is a component of the TREX (transcription/export) complex, which is involved in transcription and export of mRNAs. A missense mutation in this gene is associated with a neurodevelopmental disorder called Beaulieu-Boycott-Innes syndrome. [provided by RefSeq, Dec 2016].
Transcript (Including UTRs)
   Position: hg19 chr16:3,074,032-3,077,756 Size: 3,725 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr16:3,074,328-3,077,658 Size: 3,331 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:3,074,032-3,077,756)mRNA (may differ from genome)Protein (341 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: THOC6_HUMAN
DESCRIPTION: RecName: Full=THO complex subunit 6 homolog; AltName: Full=Functional spliceosome-associated protein 35; Short=fSAP35; AltName: Full=WD repeat-containing protein 58;
FUNCTION: Component of the THO subcomplex of the TREX complex. The TREX complex specifically associates with spliced mRNA and not with unspliced pre-mRNA. It is recruited to spliced mRNAs by a transcription-independent mechanism. Binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export. The recruitment occurs via an interaction between ALYREF/THOC4 and the cap-binding protein NCBP1. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. The recruitment of the TREX complex to the intronless viral mRNA occurs via an interaction between KSHV ORF57 protein and ALYREF/THOC4.
SUBUNIT: Component of the THO complex, which is composed of THOC1, THOC2, THOC5, THOC6 and THOC7. Together with THOC3, ALYREF/THOC4 and DDX39B, THO forms the transcription/export (TREX) complex.
SIMILARITY: Belongs to the WD repeat THOC6 family.
SIMILARITY: Contains 7 WD repeats.
SEQUENCE CAUTION: Sequence=BAG36782.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): THOC6
CDC HuGE Published Literature: THOC6

-  MalaCards Disease Associations
  MalaCards Gene Search: THOC6
Diseases sorted by gene-association score: beaulieu-boycott-innes syndrome* (1591), intellectual disability (2)
* = Manually curated disease association

-  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: 26.73 RPKM in Spleen
Total median expression: 752.55 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 -139.40296-0.471 Picture PostScript Text
3' UTR -12.0098-0.122 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
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q86W42
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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 BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Biological Process:
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0006915 apoptotic process
GO:0007275 multicellular organism development
GO:0007417 central nervous system development
GO:0008380 RNA splicing
GO:0031124 mRNA 3'-end processing
GO:0043066 negative regulation of apoptotic process
GO:0046784 viral mRNA export from host cell nucleus
GO:0051028 mRNA transport

Cellular Component:
GO:0000346 transcription export complex
GO:0000347 THO complex
GO:0000445 THO complex part of transcription export complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016604 nuclear body
GO:0016607 nuclear speck
GO:0000784 nuclear chromosome, telomeric region


-  Descriptions from all associated GenBank mRNAs
  LF210713 - JP 2014500723-A/18216: Polycomb-Associated Non-Coding RNAs.
AK310113 - Homo sapiens cDNA, FLJ17155.
LF210712 - JP 2014500723-A/18215: Polycomb-Associated Non-Coding RNAs.
BC003118 - Homo sapiens THO complex 6 homolog (Drosophila), mRNA (cDNA clone MGC:2655 IMAGE:3537243), complete cds.
AK308960 - Homo sapiens cDNA, FLJ99001.
AK314086 - Homo sapiens cDNA, FLJ94761.
JD406927 - Sequence 387951 from Patent EP1572962.
AK075330 - Homo sapiens cDNA PSEC0006 fis, clone NT2RM1000630, weakly similar to PUTATIVE SERINE/THREONINE-PROTEIN KINASE PKWA (EC 2.7.1.-).
BC050674 - Homo sapiens THO complex 6 homolog (Drosophila), mRNA (cDNA clone MGC:60218 IMAGE:6067702), complete cds.
JD129773 - Sequence 110797 from Patent EP1572962.
AL832548 - Homo sapiens mRNA; cDNA DKFZp547I2117 (from clone DKFZp547I2117).
LF340548 - JP 2014500723-A/148051: Polycomb-Associated Non-Coding RNAs.
LF340546 - JP 2014500723-A/148049: Polycomb-Associated Non-Coding RNAs.
LF340545 - JP 2014500723-A/148048: Polycomb-Associated Non-Coding RNAs.
LF340544 - JP 2014500723-A/148047: Polycomb-Associated Non-Coding RNAs.
LF340543 - JP 2014500723-A/148046: Polycomb-Associated Non-Coding RNAs.
JD056111 - Sequence 37135 from Patent EP1572962.
JD138615 - Sequence 119639 from Patent EP1572962.
JD365640 - Sequence 346664 from Patent EP1572962.
MA446290 - JP 2018138019-A/18216: Polycomb-Associated Non-Coding RNAs.
MA446289 - JP 2018138019-A/18215: Polycomb-Associated Non-Coding RNAs.
MA576125 - JP 2018138019-A/148051: Polycomb-Associated Non-Coding RNAs.
MA576123 - JP 2018138019-A/148049: Polycomb-Associated Non-Coding RNAs.
MA576122 - JP 2018138019-A/148048: Polycomb-Associated Non-Coding RNAs.
MA576121 - JP 2018138019-A/148047: Polycomb-Associated Non-Coding RNAs.
MA576120 - JP 2018138019-A/148046: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q86W42 (Reactome details) participates in the following event(s):

R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-72187 mRNA 3'-end processing
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-8953854 Metabolism of RNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2RA85, NM_024339, NP_077315, PSEC0006, Q86W42, Q8NBR1, Q9BTV9, THOC6_HUMAN, WDR58
UCSC ID: uc002ctb.2
RefSeq Accession: NM_024339
Protein: Q86W42 (aka THOC6_HUMAN)
CCDS: CCDS10491.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024339.3
exon count: 13CDS single in 3' UTR: no RNA size: 1444
ORF size: 1026CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2210.00frame shift in genome: no % Coverage: 98.34
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 162# 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.