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

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; 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

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders.
Title: Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders.
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.
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.
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.
PUF60 promotes glioblastoma progression through regulation of EGFR stability.
Title: PUF60 promotes glioblastoma progression through regulation of EGFR stability.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70666 (e-PCR)
- UniSTS:37443

WI-19511 (e-PCR)
- UniSTS:31309

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables cadherin binding	HDA more info	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

NG_033879.1 RefSeqGene

Range

5072..18043

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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
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

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

143816344..143829315 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047421582.1 → XP_047277538.1 poly(U)-binding-splicing factor PUF60 isoform X3
XM_047421578.1 → XP_047277534.1 poly(U)-binding-splicing factor PUF60 isoform X1

UniProtKB/TrEMBL

E9PL19
XM_047421583.1 → XP_047277539.1 poly(U)-binding-splicing factor PUF60 isoform X4
XM_047421579.1 → XP_047277535.1 poly(U)-binding-splicing factor PUF60 isoform X2
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
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
XM_047421580.1 → XP_047277536.1 poly(U)-binding-splicing factor PUF60 isoform X2
XM_047421581.1 → XP_047277537.1 poly(U)-binding-splicing factor PUF60 isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187571.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

293391..304748 complement

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Alternate T2T-CHM13v2.0

Genomic

NC_060932.1 Alternate T2T-CHM13v2.0

Range

144973042..144986016 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

E9PL19
XM_054360140.1 → XP_054216115.1 poly(U)-binding-splicing factor PUF60 isoform X4
XM_054360135.1 → XP_054216110.1 poly(U)-binding-splicing factor PUF60 isoform X2
XM_054360138.1 → XP_054216113.1 poly(U)-binding-splicing factor PUF60 isoform X3
XM_054360139.1 → XP_054216114.1 poly(U)-binding-splicing factor PUF60 isoform X3
XM_054360133.1 → XP_054216108.1 poly(U)-binding-splicing factor PUF60 isoform X1

UniProtKB/TrEMBL

E9PL19
XM_054360136.1 → XP_054216111.1 poly(U)-binding-splicing factor PUF60 isoform X2
XM_054360137.1 → XP_054216112.1 poly(U)-binding-splicing factor PUF60 isoform X3