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    PUF60 poly(U) binding splicing factor 60 [ Homo sapiens (human) ]

    Gene ID: 22827, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PUF60provided by HGNC
    Official Full Name
    poly(U) binding splicing factor 60provided by HGNC
    Primary source
    HGNC:HGNC:17042
    See related
    Ensembl:ENSG00000179950 MIM:604819; AllianceGenome:HGNC:17042
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FIR; VRJS; RoBPI; SIAHBP1
    Summary
    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]
    Expression
    Ubiquitous expression in brain (RPKM 18.5), testis (RPKM 17.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PUF60 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143816344..143829315, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144973042..144986016, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144898514..144911485, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene IQ motif and ankyrin repeat containing 1 Neighboring gene SREBF pathway regulator in golgi 1 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144852281-144852954 Neighboring gene scribble planar cell polarity protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144896321-144896985 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144897270-144897902 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144897903-144898535 Neighboring gene microRNA 937 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:144911577-144912776 Neighboring gene uncharacterized LOC107986985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144918993-144919720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144923032-144923762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144923763-144924492 Neighboring gene nuclear receptor binding protein 2 Neighboring gene microRNA 6845 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144939917-144940418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:144940419-144940918 Neighboring gene epiplakin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144948081-144948772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144949483-144950125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144953345-144953987

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of ribonucleoprotein (RNP)-specific protein interactions using a yeast RNP interaction trap assay (RITA). Bouffard P, et al. Biotechniques, 1999 Oct. PMID 10524322
    2. The functional response of upstream DNA to dynamic supercoiling in vivo. Kouzine F, et al. Nat Struct Mol Biol, 2008 Feb. PMID 18193062
    3. Dominant variants in the splicing factor PUF60 cause a recognizable syndrome with intellectual disability, heart defects and short stature. El Chehadeh S, et al. Eur J Hum Genet, 2016 Jan. PMID 27804958, Free PMC Article
    4. Anti-FIRs (PUF60) auto-antibodies are detected in the sera of early-stage colon cancer patients. Kobayashi S, et al. Oncotarget, 2016 Dec 13. PMID 27756887, Free PMC Article
    5. Eye coloboma and complex cardiac malformations belong to the clinical spectrum of PUF60 variants. Santos-Simarro F, et al. Clin Genet, 2017 Sep. PMID 28074499

    See all (203) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders.
      Title: Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders.
    2. PUF60 promotes cell cycle and lung cancer progression by regulating alternative splicing of CDC25C.
      Title: PUF60 promotes cell cycle and lung cancer progression by regulating alternative splicing of CDC25C.
    3. PUF60-related developmental disorder: A case series and phenotypic analysis of 10 additional patients with monoallelic PUF60 variants.
      Title: PUF60-related developmental disorder: A case series and phenotypic analysis of 10 additional patients with monoallelic PUF60 variants.
    4. The diverse pleiotropic effects of spliceosomal protein PUF60: A case series of Verheij syndrome.
      Title: The diverse pleiotropic effects of spliceosomal protein PUF60: A case series of Verheij syndrome.
    5. PUF60 promotes glioblastoma progression through regulation of EGFR stability.
      Title: PUF60 promotes glioblastoma progression through regulation of EGFR stability.
    6. Poly(U) binding splicing factor 60 promotes renal cell carcinoma growth by transcriptionally upregulating telomerase reverse transcriptase.
      Title: Poly(U) binding splicing factor 60 promotes renal cell carcinoma growth by transcriptionally upregulating telomerase reverse transcriptase.
    7. Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60.
      Title: Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60.
    8. PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RNA recognition motif.
      Title: PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.
    9. 3 Verheij syndrome patients with de novo pathogenic variants in PUF60 are described. Mutations in gene PUF60 were analyzed.
      Title: Eye coloboma and complex cardiac malformations belong to the clinical spectrum of PUF60 variants.
    10. PUF60 is involved in: 1) up-regulation of core promoter activity through its interaction with transcription factor TCF7L2, 2) promotion of 3.5 kb RNA degradation and 3) suppression of 3.5 kb RNA splicing.
      Title: Involvement of PUF60 in Transcriptional and Post-transcriptional Regulation of Hepatitis B Virus Pregenomic RNA Expression.
    Submit: New GeneRIF Correction See all GeneRIFs (28)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    8q24.3 microdeletion syndrome
    MedGen: C3810023 OMIM: 615583 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2024-01-09)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2024-01-09)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ31379

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables cadherin binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splice site recognition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    poly(U)-binding-splicing factor PUF60
    Names
    FBP interacting repressor
    FUSE-binding protein-interacting repressor
    Ro ribonucleoprotein-binding protein 1
    Siah binding protein 1
    poly(U) binding splicing factor 60KDa
    pyrimidine tract binding splicing factor

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_033879.1 RefSeqGene

      Range
      5072..18043
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136033.3 → NP_001129505.1  poly(U)-binding-splicing factor PUF60 isoform c

      See identical proteins and their annotated locations for NP_001129505.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate in-frame downstream start site, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AW249619, BC011265, BG771821
      Consensus CDS
      CCDS47935.1
      Related
      ENSP00000402953.2, ENST00000453551.6
      Conserved Domains (1) summary
      TIGR01645
      Location:1 → 516
      half-pint; poly-U binding splicing factor, half-pint family

    2. NM_001271096.2 → NP_001258025.1  poly(U)-binding-splicing factor PUF60 isoform d

      See identical proteins and their annotated locations for NP_001258025.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site and lacks an alternate exon in the coding region, compared to variant 1, but maintains the reading frame. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AC105219, AF217197, AW249619, BX418925
      Consensus CDS
      CCDS94355.1
      UniProtKB/TrEMBL
      E9PQ56
      Related
      ENSP00000432610.2, ENST00000526459.6
      Conserved Domains (1) summary
      TIGR01645
      Location:9 → 541
      half-pint; poly-U binding splicing factor, half-pint family

    3. NM_001271097.2 → NP_001258026.1  poly(U)-binding-splicing factor PUF60 isoform e

      See identical proteins and their annotated locations for NP_001258026.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5, also known as FIRdeltaexon2) lacks two alternate in-frame exons in the coding region, compared to variant 1. The encoded isoform (e) is shorter than isoform a.
      Source sequence(s)
      AF217197, AW249619, CX163878
      Consensus CDS
      CCDS59515.1
      Related
      ENSP00000431960.1, ENST00000527197.5
      Conserved Domains (1) summary
      TIGR01645
      Location:9 → 513
      half-pint; poly-U binding splicing factor, half-pint family

    4. NM_001271098.2 → NP_001258027.1  poly(U)-binding-splicing factor PUF60 isoform f

      See identical proteins and their annotated locations for NP_001258027.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (f) is shorter than isoform a.
      Source sequence(s)
      AC105219, AF217197, AL522753, AW249619
      Consensus CDS
      CCDS94356.1
      UniProtKB/TrEMBL
      H0YEM1
      Related
      ENSP00000436131.2, ENST00000527744.6
      Conserved Domains (1) summary
      TIGR01645
      Location:9 → 558
      half-pint; poly-U binding splicing factor, half-pint family

    5. NM_001271099.2 → NP_001258028.1  poly(U)-binding-splicing factor PUF60 isoform g

      See identical proteins and their annotated locations for NP_001258028.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7, also known as PUF60deltaexon2) lacks an alternate in-frame exon in the coding region, compared to variant 1. The encoded isoform (g) is shorter than isoform a.
      Source sequence(s)
      AF217197, AW249619, CT000277
      Consensus CDS
      CCDS59516.1
      Related
      ENSP00000395417.2, ENST00000456095.6
      Conserved Domains (1) summary
      TIGR01645
      Location:9 → 530
      half-pint; poly-U binding splicing factor, half-pint family

    6. NM_001271100.2 → NP_001258029.1  poly(U)-binding-splicing factor PUF60 isoform h

      See identical proteins and their annotated locations for NP_001258029.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR and contains multiple differences in the coding region, compared to variant 1. These differences result in initiation of translation at an alternate in-frame downstream start site. The encoded isoform (h) is shorter than isoform a.
      Source sequence(s)
      AW249619, BC009734, BG771821
      Consensus CDS
      CCDS59514.1
      Related
      ENSP00000322016.7, ENST00000313352.11
      Conserved Domains (1) summary
      TIGR01645
      Location:1 → 499
      half-pint; poly-U binding splicing factor, half-pint family

    7. NM_001362895.2 → NP_001349824.1  poly(U)-binding-splicing factor PUF60 isoform i

      Status: REVIEWED

      Source sequence(s)
      AC105219, AW249619, BC011265, BG771821
      Consensus CDS
      CCDS94354.1
      UniProtKB/TrEMBL
      E9PL19
      Related
      ENSP00000433403.2, ENST00000533162.2
      Conserved Domains (1) summary
      TIGR01645
      Location:44 → 596
      half-pint; poly-U binding splicing factor, half-pint family

    8. NM_001362896.2 → NP_001349825.1  poly(U)-binding-splicing factor PUF60 isoform i

      Status: REVIEWED

      Source sequence(s)
      AC105219, AW249619, BC011265, BG771821
      Consensus CDS
      CCDS94354.1
      UniProtKB/TrEMBL
      E9PL19
      Related
      ENSP00000515499.1, ENST00000703847.1
      Conserved Domains (1) summary
      TIGR01645
      Location:44 → 596
      half-pint; poly-U binding splicing factor, half-pint family

    9. NM_001362897.2 → NP_001349826.1  poly(U)-binding-splicing factor PUF60 isoform j

      Status: REVIEWED

      Source sequence(s)
      AW249619, BC011265, BQ421738
      Conserved Domains (1) summary
      TIGR01645
      Location:44 → 579
      half-pint; poly-U binding splicing factor, half-pint family

    10. NM_014281.5 → NP_055096.2  poly(U)-binding-splicing factor PUF60 isoform b

      See identical proteins and their annotated locations for NP_055096.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AF217197, AW249619, CN371576
      Consensus CDS
      CCDS47933.1
      Related
      ENSP00000322036.7, ENST00000349157.10
      Conserved Domains (1) summary
      TIGR01645
      Location:7 → 542
      half-pint; poly-U binding splicing factor, half-pint family

    11. NM_078480.3 → NP_510965.1  poly(U)-binding-splicing factor PUF60 isoform a

      See identical proteins and their annotated locations for NP_510965.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the isoform a.
      Source sequence(s)
      AF114818, AF217197, AW249619
      Consensus CDS
      CCDS47934.1
      UniProtKB/Swiss-Prot
      A8K8K8, Q969E7, Q96D94, Q96H63, Q99628, Q9NZA0, Q9UHX1, Q9UJY7
      Related
      ENSP00000434359.1, ENST00000526683.6
      Conserved Domains (1) summary
      TIGR01645
      Location:7 → 559
      half-pint; poly-U binding splicing factor, half-pint family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      143816344..143829315 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421582.1 → XP_047277538.1  poly(U)-binding-splicing factor PUF60 isoform X3

    2. XM_047421578.1 → XP_047277534.1  poly(U)-binding-splicing factor PUF60 isoform X1

      UniProtKB/TrEMBL
      E9PL19

    3. XM_047421583.1 → XP_047277539.1  poly(U)-binding-splicing factor PUF60 isoform X4

    4. XM_047421579.1 → XP_047277535.1  poly(U)-binding-splicing factor PUF60 isoform X2

    5. XM_017013236.2 → XP_016868725.1  poly(U)-binding-splicing factor PUF60 isoform X3

      Conserved Domains (1) summary
      TIGR01645
      Location:44 → 579
      half-pint; poly-U binding splicing factor, half-pint family

    6. XM_017013234.2 → XP_016868723.1  poly(U)-binding-splicing factor PUF60 isoform X1

      UniProtKB/TrEMBL
      E9PL19
      Conserved Domains (1) summary
      TIGR01645
      Location:44 → 596
      half-pint; poly-U binding splicing factor, half-pint family

    7. XM_047421580.1 → XP_047277536.1  poly(U)-binding-splicing factor PUF60 isoform X2

    8. XM_047421581.1 → XP_047277537.1  poly(U)-binding-splicing factor PUF60 isoform X3

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187571.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      293391..304748 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      144973042..144986016 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360134.1 → XP_054216109.1  poly(U)-binding-splicing factor PUF60 isoform X1

      UniProtKB/TrEMBL
      E9PL19

    2. XM_054360140.1 → XP_054216115.1  poly(U)-binding-splicing factor PUF60 isoform X4

    3. XM_054360135.1 → XP_054216110.1  poly(U)-binding-splicing factor PUF60 isoform X2

    4. XM_054360138.1 → XP_054216113.1  poly(U)-binding-splicing factor PUF60 isoform X3

    5. XM_054360139.1 → XP_054216114.1  poly(U)-binding-splicing factor PUF60 isoform X3

    6. XM_054360133.1 → XP_054216108.1  poly(U)-binding-splicing factor PUF60 isoform X1

      UniProtKB/TrEMBL
      E9PL19

    7. XM_054360136.1 → XP_054216111.1  poly(U)-binding-splicing factor PUF60 isoform X2

    8. XM_054360137.1 → XP_054216112.1  poly(U)-binding-splicing factor PUF60 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHX1.1 GenPept UniProtKB/Swiss-Prot:Q9UHX1

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