Human Gene PUF60 (uc003yzs.4) Description and Page Index
  Description: Homo sapiens poly-U binding splicing factor 60KDa (PUF60), transcript variant 1, mRNA.
RefSeq Summary (NM_078480): This gene encodes a nucleic acid-binding protein that plays a role in a variety of nuclear processes, including pre-mRNA splicing and transcriptional regulation. The encoded protein forms a complex with the far upstream DNA element (FUSE) and FUSE-binding protein at the myelocytomatosis oncogene (MYC) promoter. This complex represses MYC transcription through the core-TFIIH basal transcription factor. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2012].
Transcript (Including UTRs)
   Position: hg19 chr8:144,898,514-144,911,556 Size: 13,043 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr8:144,898,690-144,911,473 Size: 12,784 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene 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 (chr8:144,898,514-144,911,556)mRNA (may differ from genome)Protein (559 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Poly(U)-binding-splicing factor PUF60; AltName: Full=60 kDa poly(U)-binding-splicing factor; AltName: Full=FUSE-binding protein-interacting repressor; Short=FBP-interacting repressor; AltName: Full=Ro-binding protein 1; Short=RoBP1; AltName: Full=Siah-binding protein 1; Short=Siah-BP1;
FUNCTION: DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Isoform 6 failed to repress MYC transcription and inhibited FIR-induced apoptosis in colorectal cancer. Isoform 6 may contribute to tumor progression by enabling increased MYC expression and greater resistance to apoptosis in tumors than in normal cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA.
SUBUNIT: Homodimer. Associates with the spliceosome. Found in a complex with TROVE2 and Y5 RNA. Found in a complex with FUBP1 and far upstream element (FUSE) DNA segment. Interacts directly with ERCC3. Interacts with CDK7, GTF2H1 and SFRS11. Does not interact with ERCC3 in xeroderma pigmentosum complementation group B (XPB) cells.
INTERACTION: O00555:CACNA1A; NbExp=2; IntAct=EBI-1053259, EBI-766279; Q15365:PCBP1; NbExp=2; IntAct=EBI-1053259, EBI-946095; Q96I34:PPP1R16A; NbExp=2; IntAct=EBI-1053259, EBI-710402; Q9UHR5:SAP30BP; NbExp=4; IntAct=EBI-1053259, EBI-751683;
SUBCELLULAR LOCATION: Nucleus. Note=Colocalizes partially with TROVE2.
TISSUE SPECIFICITY: Isoform 2 is expressed in colonic epithelium and colorectal epithelium cancer (at protein level). Isoform 6 is expressed in colorectal epithelial cancer but below detection level in colonic epithelium. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon and peripheral blood leukocytes.
DOMAIN: The third RNA recognition motif, called PUMP domain, is atypical and may rather mediate homodimerization and/or protein- protein interactions.
MISCELLANEOUS: Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells.
SIMILARITY: Belongs to the RRM half pint family.
SIMILARITY: Contains 3 RRM (RNA recognition motif) domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: PUF60
Diseases sorted by gene-association score: verheij syndrome* (1228), coloboma (10)
* = 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: 40.63 RPKM in Nerve - Tibial
Total median expression: 1285.15 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 -28.8083-0.347 Picture PostScript Text
3' UTR -58.60176-0.333 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR006532 - PolyU-bd
IPR000504 - RRM_dom
IPR003954 - RRM_dom_euk

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

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



To conserve bandwidth, only the images from the first 3 structures are shown.
2QFJ - X-ray MuPIT 3DXB - X-ray 3UE2 - X-ray MuPIT
3US5 - X-ray MuPIT 3UWT - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9UHX1
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    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:0045296 cadherin binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006397 mRNA processing
GO:0006915 apoptotic process
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0030054 cell junction
GO:0019907 cyclin-dependent protein kinase activating kinase holoenzyme complex

-  Descriptions from all associated GenBank mRNAs
  BC011979 - Homo sapiens poly-U binding splicing factor 60KDa, mRNA (cDNA clone MGC:9835 IMAGE:3863660), complete cds.
BC035435 - Homo sapiens poly-U binding splicing factor 60KDa, mRNA (cDNA clone IMAGE:4154228).
BC009734 - Homo sapiens poly-U binding splicing factor 60KDa, mRNA (cDNA clone MGC:9958 IMAGE:3877563), complete cds.
U51586 - Human siah binding protein 1 (SiahBP1) mRNA, partial cds.
AF190744 - Homo sapiens poly-U binding splicing factor PUF60 (PUF60) mRNA, partial cds.
AF217197 - Homo sapiens FBP-interacting repressor (FIR) mRNA, complete cds.
BC008875 - Homo sapiens poly-U binding splicing factor 60KDa, mRNA (cDNA clone MGC:15202 IMAGE:4138778), complete cds.
AF114818 - Homo sapiens Ro ribonucleoprotein-binding protein 1 mRNA, complete cds.
BC011265 - Homo sapiens poly-U binding splicing factor 60KDa, mRNA (cDNA clone MGC:18191 IMAGE:4155549), complete cds.
JD395932 - Sequence 376956 from Patent EP1572962.
AK292373 - Homo sapiens cDNA FLJ77377 complete cds, highly similar to Homo sapiens fuse-binding protein-interacting repressor (SIAHBP1), transcript variant 1, mRNA.
KJ893297 - Synthetic construct Homo sapiens clone ccsbBroadEn_02691 PUF60 gene, encodes complete protein.
KJ902235 - Synthetic construct Homo sapiens clone ccsbBroadEn_11629 PUF60 gene, encodes complete protein.
KJ893296 - Synthetic construct Homo sapiens clone ccsbBroadEn_02690 PUF60 gene, encodes complete protein.
AB527889 - Synthetic construct DNA, clone: pF1KB0473, Homo sapiens PUF60 gene for poly-U binding splicing factor 60KDa, without stop codon, in Flexi system.
CR457143 - Homo sapiens full open reading frame cDNA clone RZPDo834F1014D for gene SIAHBP1, fuse-binding protein-interacting repressor; complete cds, incl. stopcodon.
JD021108 - Sequence 2132 from Patent EP1572962.
JD028709 - Sequence 9733 from Patent EP1572962.
AK055941 - Homo sapiens cDNA FLJ31379 fis, clone NHNPC1000084, highly similar to Homo sapiens poly-U binding splicing factor PUF60 mRNA.
CU679467 - Synthetic construct Homo sapiens gateway clone IMAGE:100019689 5' read PUF60 mRNA.
CU679161 - Synthetic construct Homo sapiens gateway clone IMAGE:100017397 5' read PUF60 mRNA.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q9UHX1 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K8K8, FIR, NM_078480, NP_510965, PUF60_HUMAN, Q969E7, Q96D94, Q96H63, Q99628, Q9NZA0, Q9UHX1, Q9UJY7, ROBPI, SIAHBP1, uc003yzs.3
UCSC ID: uc003yzs.4
RefSeq Accession: NM_078480
Protein: Q9UHX1 (aka PUF60_HUMAN)
CCDS: CCDS47933.1, CCDS47934.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_078480.2
exon count: 12CDS single in 3' UTR: no RNA size: 1948
ORF size: 1680CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3560.00frame shift in genome: no % Coverage: 99.54
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.