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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
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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 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
not available

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)

Genotypes

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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