Human Gene THOC5 (uc003afs.3) Description and Page Index
  Description: Homo sapiens THO complex 5 (THOC5), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr22:29,904,156-29,949,644 Size: 45,489 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr22:29,904,446-29,945,136 Size: 40,691 Coding Exon Count: 19 

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 (chr22:29,904,156-29,949,644)mRNA (may differ from genome)Protein (683 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: THOC5_HUMAN
DESCRIPTION: RecName: Full=THO complex subunit 5 homolog; AltName: Full=Functional spliceosome-associated protein 79; Short=fSAP79; AltName: Full=NF2/meningioma region protein pK1.3; AltName: Full=Placental protein 39.2; Short=PP39.2; AltName: Full=hTREX90;
FUNCTION: Component 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. 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 beteen KSHV ORF57 protein and ALYREF/THOC4. DDX39B functions as a bridge between ALYREF/THOC4 and the THO complex. THOC5 in conjunction with ALYREF/THOC4 functions in NXF1-NXT1 mediated nuclear export of HSP70 mRNA. Regulates the expression of myeloid transcription factors CEBPA, CEBPB and GAB2 by enhancing the levels of phosphatidylinositol 3,4,5-trisphosphate. May be involved in the differentiation of granulocytes and adipocytes. Essential for hematopoietic primitive cell survival and plays an integral role in monocytic development.
SUBUNIT: Interacts with phosphorylated CSF1R and THOC1 (By similarity). 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. Interacts with ALYREF/THOC4 and THOC7. Interacts (via N- terminus) with the NTF2 domain of NXF1. Forms a complex with CEBPB (By similarity).
SUBCELLULAR LOCATION: Nucleus. Cytoplasm (By similarity). Note=Shuttles between nucleus and cytoplasm.
TISSUE SPECIFICITY: Ubiquitously expressed.
PTM: Phosphorylated on tyrosine upon binding to activated CSF1R; which causes a dissociation of the two proteins. Phosphorylation on Ser-5 and/or Ser-6 is required for nuclear export. Phosphorylated on Thr-328 in insulin-stimulated adipocytes (By similarity). Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the THOC5 family.
SEQUENCE CAUTION: Sequence=BAA76827.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): THOC5
CDC HuGE Published Literature: THOC5
Positive Disease Associations: Carotid atherosclerosis in HIV infection
Related Studies:
  1. Carotid atherosclerosis in HIV infection
    Shrestha ,et al. 2010, A genome-wide association study of carotid atherosclerosis in HIV-infected men, AIDS (London, England) 2009 . [PubMed 20009918]
    These results suggest that in the context of HIV infection and HAART, a functional SNP in a biologically plausible candidate gene, RYR3, is associated with increased common carotid IMT, which is a surrogate for atherosclerosis.

-  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: 10.16 RPKM in Uterus
Total median expression: 268.16 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 -98.60219-0.450 Picture PostScript Text
3' UTR -94.70290-0.327 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
IPR019163 - THO_Thoc5

Pfam Domains:
PF09766 - Fms-interacting protein

ModBase Predicted Comparative 3D Structure on Q13769
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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 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:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding

Biological Process:
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0008380 RNA splicing
GO:0030154 cell differentiation
GO:0030224 monocyte differentiation
GO:0031124 mRNA 3'-end processing
GO:0032786 positive regulation of DNA-templated transcription, elongation
GO:0046784 viral mRNA export from host cell nucleus
GO:0051028 mRNA transport
GO:0060215 primitive hemopoiesis
GO:2000002 negative regulation of DNA damage checkpoint

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:0005737 cytoplasm
GO:0000784 nuclear chromosome, telomeric region


-  Descriptions from all associated GenBank mRNAs
  AB023200 - Homo sapiens KIAA0983 mRNA for KIAA0983 protein.
LF384706 - JP 2014500723-A/192209: Polycomb-Associated Non-Coding RNAs.
JD369176 - Sequence 350200 from Patent EP1572962.
JD469157 - Sequence 450181 from Patent EP1572962.
JD536059 - Sequence 517083 from Patent EP1572962.
JD460464 - Sequence 441488 from Patent EP1572962.
AK098709 - Homo sapiens cDNA FLJ25843 fis, clone TST08717, highly similar to Gene from NF2/meningioma region of 22q12.
AK122673 - Homo sapiens cDNA FLJ16118 fis, clone ASTRO2013585.
BC003615 - Homo sapiens THO complex 5, mRNA (cDNA clone MGC:1540 IMAGE:2988049), complete cds.
AK025385 - Homo sapiens cDNA: FLJ21732 fis, clone COLF1867.
AK225752 - Homo sapiens mRNA for Fms-interacting protein variant, clone: FCC135F06.
CR456542 - Homo sapiens PK1.3 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.PK1.3).
JD368051 - Sequence 349075 from Patent EP1572962.
JD185676 - Sequence 166700 from Patent EP1572962.
JD067921 - Sequence 48945 from Patent EP1572962.
JD185675 - Sequence 166699 from Patent EP1572962.
KJ897870 - Synthetic construct Homo sapiens clone ccsbBroadEn_07264 THOC5 gene, encodes complete protein.
CU013142 - Homo sapiens THOC5, mRNA (cDNA clone IMAGE:100000495), complete cds, with stop codon, in Gateway system.
AB463311 - Synthetic construct DNA, clone: pF1KA0983, Homo sapiens THOC5 gene for THO complex 5, without stop codon, in Flexi system.
CU013430 - Homo sapiens THOC5, mRNA (cDNA clone IMAGE:100000399), complete cds, without stop codon, in Gateway system.
AJ006069 - Homo sapiens mRNA for placental protein 39.2, partial.
LF324701 - JP 2014500723-A/132204: Polycomb-Associated Non-Coding RNAs.
LF324698 - JP 2014500723-A/132201: Polycomb-Associated Non-Coding RNAs.
AK225169 - Homo sapiens mRNA for Fms-interacting protein variant, clone: CBR04236.
LF324696 - JP 2014500723-A/132199: Polycomb-Associated Non-Coding RNAs.
MA620283 - JP 2018138019-A/192209: Polycomb-Associated Non-Coding RNAs.
MA560278 - JP 2018138019-A/132204: Polycomb-Associated Non-Coding RNAs.
MA560275 - JP 2018138019-A/132201: Polycomb-Associated Non-Coding RNAs.
MA560273 - JP 2018138019-A/132199: Polycomb-Associated Non-Coding RNAs.

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

Protein Q13769 (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: C22orf19, KIAA0983, NM_001002879, NP_003669, O60839, Q13769, Q9UPZ5, THOC5_HUMAN
UCSC ID: uc003afs.3
RefSeq Accession: NM_001002879
Protein: Q13769 (aka THOC5_HUMAN)
CCDS: CCDS13859.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001002879.1
exon count: 20CDS single in 3' UTR: no RNA size: 2578
ORF size: 2052CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4196.00frame shift in genome: no % Coverage: 99.34
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.