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

Gene ID: 22827, updated on 10-Oct-2020

Summary

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
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

Genomic context

See PUF60 in Genome Data Viewer
Location:
8q24.3
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (143816344..143829315, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144898514..144911556, 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 scribble planar cell polarity protein Neighboring gene microRNA 937 Neighboring gene uncharacterized LOC107986985 Neighboring gene nuclear receptor binding protein 2 Neighboring gene microRNA 6845 Neighboring gene epiplakin 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ31379

Gene Ontology Provided by GOA

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

General protein information

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)

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_001136033.3NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Related
    ENSP00000402953.2, ENST00000453551.6
    Conserved Domains (1) summary
    TIGR01645
    Location:1516
    half-pint; poly-U binding splicing factor, half-pint family
  2. NM_001271096.2NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Conserved Domains (1) summary
    TIGR01645
    Location:9541
    half-pint; poly-U binding splicing factor, half-pint family
  3. NM_001271097.2NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Related
    ENSP00000431960.1, ENST00000527197.5
    Conserved Domains (1) summary
    TIGR01645
    Location:9513
    half-pint; poly-U binding splicing factor, half-pint family
  4. NM_001271098.2NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Conserved Domains (1) summary
    TIGR01645
    Location:9558
    half-pint; poly-U binding splicing factor, half-pint family
  5. NM_001271099.2NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Related
    ENSP00000395417.2, ENST00000456095.6
    Conserved Domains (1) summary
    TIGR01645
    Location:9530
    half-pint; poly-U binding splicing factor, half-pint family
  6. NM_001271100.2NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Related
    ENSP00000322016.7, ENST00000313352.11
    Conserved Domains (1) summary
    TIGR01645
    Location:1499
    half-pint; poly-U binding splicing factor, half-pint family
  7. NM_001362895.2NP_001349824.1  poly(U)-binding-splicing factor PUF60 isoform i

    Status: REVIEWED

    Source sequence(s)
    AC105219, AW249619, BC011265, BG771821
    Conserved Domains (1) summary
    TIGR01645
    Location:44596
    half-pint; poly-U binding splicing factor, half-pint family
  8. NM_001362896.2NP_001349825.1  poly(U)-binding-splicing factor PUF60 isoform i

    Status: REVIEWED

    Source sequence(s)
    AC105219, AW249619, BC011265, BG771821
    Conserved Domains (1) summary
    TIGR01645
    Location:44596
    half-pint; poly-U binding splicing factor, half-pint family
  9. NM_001362897.2NP_001349826.1  poly(U)-binding-splicing factor PUF60 isoform j

    Status: REVIEWED

    Source sequence(s)
    AW249619, BC011265, BQ421738
    Conserved Domains (1) summary
    TIGR01645
    Location:44579
    half-pint; poly-U binding splicing factor, half-pint family
  10. NM_014281.5NP_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
    UniProtKB/Swiss-Prot
    Q9UHX1
    Related
    ENSP00000322036.7, ENST00000349157.10
    Conserved Domains (1) summary
    TIGR01645
    Location:7542
    half-pint; poly-U binding splicing factor, half-pint family
  11. NM_078480.3NP_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
    Q9UHX1
    Related
    ENSP00000434359.1, ENST00000526683.6
    Conserved Domains (1) summary
    TIGR01645
    Location:7559
    half-pint; poly-U binding splicing factor, half-pint family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017013236.1XP_016868725.1  poly(U)-binding-splicing factor PUF60 isoform X9

    Conserved Domains (1) summary
    TIGR01645
    Location:44579
    half-pint; poly-U binding splicing factor, half-pint family
  2. XM_017013234.1XP_016868723.1  poly(U)-binding-splicing factor PUF60 isoform X5

    Conserved Domains (1) summary
    TIGR01645
    Location:44596
    half-pint; poly-U binding splicing factor, half-pint family
  3. XM_017013240.1XP_016868729.1  poly(U)-binding-splicing factor PUF60 isoform X14

    UniProtKB/Swiss-Prot
    Q9UHX1
    Conserved Domains (1) summary
    TIGR01645
    Location:1499
    half-pint; poly-U binding splicing factor, half-pint family
  4. XM_017013239.1XP_016868728.1  poly(U)-binding-splicing factor PUF60 isoform X13

    UniProtKB/Swiss-Prot
    Q9UHX1
    Conserved Domains (1) summary
    TIGR01645
    Location:1516
    half-pint; poly-U binding splicing factor, half-pint family
  5. XM_017013235.1XP_016868724.1  poly(U)-binding-splicing factor PUF60 isoform X6

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_187571.1 Reference GRCh38.p13 ALT_REF_LOCI_1

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