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Aliases for PUF60 Gene

Aliases for PUF60 Gene

  • Poly(U) Binding Splicing Factor 60 2 3 5
  • FUSE-Binding Protein-Interacting Repressor 3 4
  • Pyrimidine Tract Binding Splicing Factor 2 3
  • Poly(U) Binding Splicing Factor 60KDa 2 3
  • FBP Interacting Repressor 2 3
  • Siah Binding Protein 1 2 3
  • SIAHBP1 3 4
  • RoBPI 3 4
  • FIR 3 4
  • Ro Ribonucleoprotein Binding Protein 1 2
  • Ro Ribonucleoprotein-Binding Protein 1 3
  • 60 KDa Poly(U)-Binding-Splicing Factor 4
  • Poly(U)-Binding-Splicing Factor PUF60 3
  • FBP-Interacting Repressor 4
  • Siah-Binding Protein 1 4
  • Ro-Binding Protein 1 4
  • Siah-BP1 4
  • RoBP1 4
  • VRJS 3

External Ids for PUF60 Gene

Previous GeneCards Identifiers for PUF60 Gene

  • GC08M144971
  • GC08M144898
  • GC08M140151

Summaries for PUF60 Gene

Entrez Gene Summary for PUF60 Gene

  • 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]

GeneCards Summary for PUF60 Gene

PUF60 (Poly(U) Binding Splicing Factor 60) is a Protein Coding gene. Diseases associated with PUF60 include Verheij Syndrome. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include nucleic acid binding and identical protein binding. An important paralog of this gene is RBM39.

UniProtKB/Swiss-Prot for PUF60 Gene

  • 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.

Gene Wiki entry for PUF60 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PUF60 Gene

Genomics for PUF60 Gene

Regulatory Elements for PUF60 Gene

Enhancers for PUF60 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08F143964 1.2 FANTOM5 Ensembl ENCODE 10.7 -136.3 -136289 3.6 PKNOX1 HLF SIN3A MNT CEBPG ZNF592 HIC1 CTBP1 GATA3 GLIS1 PLEC PARP10 SPATC1 EXOSC4 ENSG00000255224 MIR6847 EPPK1 PUF60 C8orf82 C8orf31
GH08F143826 1.1 ENCODE 10.4 +1.1 1114 3.6 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 KLF13 ZNF263 ZNF251 ZNF517 LRRC14 ZNF696 ZNF623 ZNF34 MINCR PUF60 LOC105375803 RHPN1
GH08F143820 1.2 Ensembl ENCODE 9.5 +6.5 6471 5.6 ARID4B ZNF48 ZSCAN9 RAD21 YY1 RARA ZNF121 SCRT2 EGR2 THAP11 LRRC14 ZNF517 ADCK5 VPS28 LOC105375803 ZNF696 ZNF251 PUF60 BREA2 MIR937
GH08F144002 1.1 Ensembl ENCODE 10.3 -174.6 -174645 3.5 HDAC1 PKNOX1 SAP130 MAX CEBPG THRB RAD21 YY1 GATA3 SCRT2 PLEC WDR97 EXOSC4 MIR6847 ENSG00000255224 MIR661 GPAA1 CYC1 MAF1 SHARPIN
GH08F143905 0.9 ENCODE 11.9 -76.4 -76400 1.5 HDAC1 ELF3 TBP ARID4B DMAP1 ZNF48 RAD21 RARA SLC30A9 CBX5 PLEC EPPK1 PUF60 MIR661 NRBP2 MIR6845 MIR937 SCRIB SPATC1 PARP10
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PUF60 on UCSC Golden Path with GeneCards custom track

Promoters for PUF60 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001446397 759 1401 PKNOX1 CREB3L1 MLX ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 KLF13

Genomic Location for PUF60 Gene

Chromosome:
8
Start:
143,816,344 bp from pter
End:
143,829,859 bp from pter
Size:
13,516 bases
Orientation:
Minus strand

Genomic View for PUF60 Gene

Genes around PUF60 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PUF60 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PUF60 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PUF60 Gene

Proteins for PUF60 Gene

  • Protein details for PUF60 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UHX1-PUF60_HUMAN
    Recommended name:
    Poly(U)-binding-splicing factor PUF60
    Protein Accession:
    Q9UHX1
    Secondary Accessions:
    • A8K8K8
    • Q969E7
    • Q96D94
    • Q96H63
    • Q99628
    • Q9NZA0
    • Q9UJY7

    Protein attributes for PUF60 Gene

    Size:
    559 amino acids
    Molecular mass:
    59875 Da
    Quaternary structure:
    • 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.
    Miscellaneous:
    • Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells.

    Three dimensional structures from OCA and Proteopedia for PUF60 Gene

    Alternative splice isoforms for PUF60 Gene

neXtProt entry for PUF60 Gene

Post-translational modifications for PUF60 Gene

  • Ubiquitination at Lys 243
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PUF60 Gene

Domains & Families for PUF60 Gene

Gene Families for PUF60 Gene

Suggested Antigen Peptide Sequences for PUF60 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UHX1

UniProtKB/Swiss-Prot:

PUF60_HUMAN :
  • The third RNA recognition motif, called PUMP domain, is atypical and may rather mediate homodimerization and/or protein-protein interactions.
  • Belongs to the RRM half pint family.
Domain:
  • The third RNA recognition motif, called PUMP domain, is atypical and may rather mediate homodimerization and/or protein-protein interactions.
  • Contains 3 RRM (RNA recognition motif) domains.
Family:
  • Belongs to the RRM half pint family.
genes like me logo Genes that share domains with PUF60: view

Function for PUF60 Gene

Molecular function for PUF60 Gene

UniProtKB/Swiss-Prot 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.

Gene Ontology (GO) - Molecular Function for PUF60 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 16169070
genes like me logo Genes that share ontologies with PUF60: view
genes like me logo Genes that share phenotypes with PUF60: view

Human Phenotype Ontology for PUF60 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for PUF60 Gene

miRTarBase miRNAs that target PUF60

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for PUF60 Gene

Localization for PUF60 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PUF60 Gene

Nucleus. Note=Colocalizes partially with TROVE2.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PUF60 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for PUF60 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005913 cell-cell adherens junction IDA 25468996
GO:0019907 colocalizes_with cyclin-dependent protein kinase activating kinase holoenzyme complex IDA 11445587
GO:0030054 cell junction IDA --
genes like me logo Genes that share ontologies with PUF60: view

Pathways & Interactions for PUF60 Gene

genes like me logo Genes that share pathways with PUF60: view

Pathways by source for PUF60 Gene

Gene Ontology (GO) - Biological Process for PUF60 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006397 mRNA processing IEA --
GO:0006915 apoptotic process IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with PUF60: view

No data available for SIGNOR curated interactions for PUF60 Gene

Drugs & Compounds for PUF60 Gene

(1) Additional Compounds for PUF60 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Pyrimidine
  • 1,3-Diazabenzene
  • 1,3-Diazine
  • M-Diazine
  • Metadiazine
  • Miazine
25247-63-6
genes like me logo Genes that share compounds with PUF60: view

Transcripts for PUF60 Gene

Unigene Clusters for PUF60 Gene

Poly-U binding splicing factor 60KDa:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PUF60 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b · 11c · 11d ^ 12a · 12b · 12c · 12d ^ 13 ^ 14 ^ 15a · 15b ^ 16
SP1: - - - - -
SP2: - - - - - -
SP3: - - - -
SP4: - - - - - -
SP5: - - - - - -
SP6: - - - - - - -
SP7: -
SP8: -
SP9: -
SP10: - - - - -
SP11: - -
SP12: -

Relevant External Links for PUF60 Gene

GeneLoc Exon Structure for
PUF60
ECgene alternative splicing isoforms for
PUF60

Expression for PUF60 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PUF60 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PUF60 Gene

This gene is overexpressed in Bone (8.5) and Peripheral blood mononuclear cells (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PUF60 Gene



Protein tissue co-expression partners for PUF60 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PUF60 Gene:

PUF60

SOURCE GeneReport for Unigene cluster for PUF60 Gene:

Hs.521924

mRNA Expression by UniProt/SwissProt for PUF60 Gene:

Q9UHX1-PUF60_HUMAN
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.
genes like me logo Genes that share expression patterns with PUF60: view

Primer Products

No data available for mRNA differential expression in normal tissues for PUF60 Gene

Orthologs for PUF60 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PUF60 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PUF60 34 35
  • 99.64 (n)
oppossum
(Monodelphis domestica)
Mammalia PUF60 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PUF60 34 35
  • 92.65 (n)
cow
(Bos Taurus)
Mammalia PUF60 34 35
  • 91.95 (n)
rat
(Rattus norvegicus)
Mammalia Puf60 34
  • 90.38 (n)
mouse
(Mus musculus)
Mammalia Puf60 34 16 35
  • 90.1 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PUF60 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves PUF60 34 35
  • 84.07 (n)
lizard
(Anolis carolinensis)
Reptilia PUF60 35
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia puf60 34
  • 81.81 (n)
Str.6194 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.6828 34
zebrafish
(Danio rerio)
Actinopterygii puf60b 35
  • 77 (a)
OneToMany
puf60a 34 35
  • 76.37 (n)
wufb33e11 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12298 34
fruit fly
(Drosophila melanogaster)
Insecta pUf68 34 35
  • 65.38 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010553 34
  • 61.17 (n)
worm
(Caenorhabditis elegans)
Secernentea rnp-6 34 35
  • 54.04 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HSH49 35
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 53 (a)
OneToMany
CSA.10424 35
  • 46 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12016 34
Species where no ortholog for PUF60 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PUF60 Gene

ENSEMBL:
Gene Tree for PUF60 (if available)
TreeFam:
Gene Tree for PUF60 (if available)

Paralogs for PUF60 Gene

Paralogs for PUF60 Gene

genes like me logo Genes that share paralogs with PUF60: view

Variants for PUF60 Gene

Sequence variations from dbSNP and Humsavar for PUF60 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs398123001 Verheij syndrome (VRJS) [MIM:615583], Pathogenic 143,818,378(-) TGAAG(C/T)ACAAG reference, missense
rs10091538 -- 143,829,011(+) CGCCA(C/G)GCTCG intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs111488010 -- 143,819,046(+) CAGAT(A/G)GGGGC intron-variant
rs111677763 -- 143,817,793(+) GGCAG(A/C/G)AGCAG intron-variant
rs111831540 -- 143,819,438(+) TGTGG(A/G)CCAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PUF60 Gene

Variant ID Type Subtype PubMed ID
nsv1161815 CNV deletion 26073780
nsv466009 CNV loss 19166990
nsv475873 CNV novel sequence insertion 20440878
nsv476765 CNV novel sequence insertion 20440878
nsv612895 CNV loss 21841781
nsv612896 CNV loss 21841781
nsv612897 CNV loss 21841781
nsv6442 CNV deletion 18451855
nsv950014 CNV deletion 24416366

Variation tolerance for PUF60 Gene

Residual Variation Intolerance Score: 11.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.30; 6.76% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PUF60 Gene

Human Gene Mutation Database (HGMD)
PUF60
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PUF60

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PUF60 Gene

Disorders for PUF60 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PUF60 Gene - From: OMIM, ClinVar, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
verheij syndrome
  • chromosome 8q24.3 deletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PUF60 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PUF60_HUMAN
  • Verheij syndrome (VRJS) [MIM:615583]: A syndrome characterized by growth retardation, delayed psychomotor development, dysmorphic facial features, and skeletal, mainly vertebral, abnormalities. Additional variable features may include coloboma, renal defects, and cardiac defects. {ECO:0000269 PubMed:24140112}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PUF60

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PUF60
genes like me logo Genes that share disorders with PUF60: view

No data available for Genatlas for PUF60 Gene

Publications for PUF60 Gene

  1. Interaction cloning and characterization of RoBPI, a novel protein binding to human Ro ribonucleoproteins. (PMID: 10668799) Bouffard P. … Boire G. (RNA 2000) 2 3 4 22 64
  2. Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF. (PMID: 17579712) Hastings M.L. … Krainer A.R. (PLoS ONE 2007) 2 3 4 64
  3. The FBP interacting repressor targets TFIIH to inhibit activated transcription. (PMID: 10882074) Liu J. … Levens D. (Mol. Cell 2000) 2 3 4 64
  4. SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant. (PMID: 24140112) Dauber A. … Katsanis N. (Am. J. Hum. Genet. 2013) 3 4 64
  5. c-myc suppressor FBP-interacting repressor for cancer diagnosis and therapy. (PMID: 19273283) Matsushita K. … Nomura F. (Front Biosci (Landmark Ed) 2009) 3 22 64

Products for PUF60 Gene

Sources for PUF60 Gene

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