Human Gene SKIC8 (ENST00000267973.7) from GENCODE V44
  Description: Homo sapiens WD repeat domain 61 (WDR61), transcript variant 2, mRNA. (from RefSeq NM_025234)
RefSeq Summary (NM_025234): WDR61 is a subunit of the human PAF and SKI complexes, which function in transcriptional regulation and are involved in events downstream of RNA synthesis, such as RNA surveillance (Zhu et al., 2005 [PubMed 16024656]).[supplied by OMIM, Mar 2008].
Gencode Transcript: ENST00000267973.7
Gencode Gene: ENSG00000140395.9
Transcript (Including UTRs)
   Position: hg38 chr15:78,283,235-78,299,609 Size: 16,375 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr15:78,283,432-78,295,686 Size: 12,255 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:78,283,235-78,299,609)mRNA (may differ from genome)Protein (305 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
LynxMalacardsMGIneXtProtOMIMPubMed
ReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WDR61_HUMAN
DESCRIPTION: RecName: Full=WD repeat-containing protein 61; AltName: Full=Meiotic recombination REC14 protein homolog; AltName: Full=SKI8 homolog; Short=Ski8;
FUNCTION: Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non- phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of MLL1; it promotes leukemogenesis though association with MLL-rearranged oncoproteins, such as MLL-MLLT3/AF9 and MLL-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3), dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1C.
SUBUNIT: Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Component of the SKI complex which consists of WDR61, SKIV2L and TTC37.
INTERACTION: Q6PD62:CTR9; NbExp=9; IntAct=EBI-358545, EBI-1019583;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm (Probable).
SIMILARITY: Contains 7 WD repeats.

-  Primer design for this transcript
 

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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.34 RPKM in Pituitary
Total median expression: 796.66 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 -33.9087-0.390 Picture PostScript Text
3' UTR -36.90197-0.187 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
IPR020472 - G-protein_beta_WD-40_rep
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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3OW8 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9GZS3
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-  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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

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

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0016055 Wnt signaling pathway
GO:0016567 protein ubiquitination
GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0045638 negative regulation of myeloid cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051571 positive regulation of histone H3-K4 methylation
GO:0080182 histone H3-K4 trimethylation
GO:2001162 positive regulation of histone H3-K79 methylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016593 Cdc73/Paf1 complex
GO:0035327 transcriptionally active chromatin
GO:0055087 Ski complex


-  Descriptions from all associated GenBank mRNAs
  LF208497 - JP 2014500723-A/16000: Polycomb-Associated Non-Coding RNAs.
MA444074 - JP 2018138019-A/16000: Polycomb-Associated Non-Coding RNAs.
AK025098 - Homo sapiens cDNA FLJ21445 fis, A-COL04457.
BC010080 - Homo sapiens WD repeat domain 61, mRNA (cDNA clone MGC:19469 IMAGE:4329599), complete cds.
AK024754 - Homo sapiens cDNA: FLJ21101 fis, clone CAS04682.
AF100786 - Homo sapiens G protein beta subunit-like protein mRNA, complete cds.
AF127799 - Homo sapiens G protein beta subunit-like protein mRNA, complete cds.
AF309553 - Homo sapiens meiotic recombination protein REC14 mRNA, complete cds.
CR457333 - Homo sapiens full open reading frame cDNA clone RZPDo834H0413D for gene REC14, recombination protein REC14; complete cds, incl. stopcodon.
HQ447187 - Synthetic construct Homo sapiens clone IMAGE:100070481; CCSB006964_02 WD repeat domain 61 (WDR61) gene, encodes complete protein.
KJ899642 - Synthetic construct Homo sapiens clone ccsbBroadEn_09036 WDR61 gene, encodes complete protein.
CU679601 - Synthetic construct Homo sapiens gateway clone IMAGE:100018096 5' read WDR61 mRNA.
LF377090 - JP 2014500723-A/184593: Polycomb-Associated Non-Coding RNAs.
MA612667 - JP 2018138019-A/184593: Polycomb-Associated Non-Coding RNAs.
LF377091 - JP 2014500723-A/184594: Polycomb-Associated Non-Coding RNAs.
MA612668 - JP 2018138019-A/184594: Polycomb-Associated Non-Coding RNAs.
AK300838 - Homo sapiens cDNA FLJ50697 complete cds.
AK304617 - Homo sapiens cDNA FLJ61675 complete cds, highly similar to WD repeat protein 61.
AK311320 - Homo sapiens cDNA, FLJ18362.
AK310477 - Homo sapiens cDNA, FLJ17519.
AL109709 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 43432.
LF377099 - JP 2014500723-A/184602: Polycomb-Associated Non-Coding RNAs.
MA612676 - JP 2018138019-A/184602: Polycomb-Associated Non-Coding RNAs.
JD495990 - Sequence 477014 from Patent EP1572962.
JD229559 - Sequence 210583 from Patent EP1572962.
JD443264 - Sequence 424288 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

Reactome (by CSHL, EBI, and GO)

Protein Q9GZS3 (Reactome details) participates in the following event(s):

R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-8942099 RNF20:RNF40 binds PAF complex, Ubiquitin:UBE2A,B (Ubiquitin:RAD6), WAC and Histone H2B
R-HSA-113429 Elongating transcript encounters a lesion in the template
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-430028 Exosome Complex hydrolyzes mRNA by 3' to 5' exoribonuclease digestion
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-8852135 Protein ubiquitination
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-597592 Post-translational protein modification
R-HSA-74160 Gene expression (Transcription)
R-HSA-429958 mRNA decay by 3' to 5' exoribonuclease
R-HSA-392499 Metabolism of proteins
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: D3DW84, ENST00000267973.1, ENST00000267973.2, ENST00000267973.3, ENST00000267973.4, ENST00000267973.5, ENST00000267973.6, NM_025234, Q6IA22, Q7Z4X4, Q9GZS3, uc002bdn.1, uc002bdn.2, uc002bdn.3, uc002bdn.4, uc002bdn.5, WDR61, WDR61_HUMAN
UCSC ID: ENST00000267973.7
RefSeq Accession: NM_025234
Protein: Q9GZS3 (aka WDR61_HUMAN)
CCDS: CCDS10300.1

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