PRPF6 pre-mRNA processing factor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRPF6provided by HGNC
Official Full Name: pre-mRNA processing factor 6provided by HGNC
Primary source: HGNC:HGNC:15860
See related: Ensembl:ENSG00000101161 MIM:613979; AllianceGenome:HGNC:15860
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: TOM; ANT1; Prp6; RP60; ANT-1; hPrp6; U5-102K; C20orf14; SNRNP102
Summary: The protein encoded by this gene appears to be involved in pre-mRNA splicing, possibly acting as a bridging factor between U5 and U4/U6 snRNPs in formation of the spliceosome. The encoded protein also can bind androgen receptor, providing a link between transcriptional activation and splicing. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 30.6), ovary (RPKM 27.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.33

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (63981132..64033100)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (65800894..65853046)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (62612485..62664453)

Chromosome 20 - NC_000020.11 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 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?

Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome.
Title: Pathogenic Variants in USH1G/SANS Alter Protein Interaction with Pre-RNA Processing Factors PRPF6 and PRPF31 of the Spliceosome.
PRPF6 promotes metastasis and paclitaxel resistance of ovarian cancer via SNHG16/CEBPB/GATA3 axis.
Title: PRPF6 promotes metastasis and paclitaxel resistance of ovarian cancer via SNHG16/CEBPB/GATA3 axis.
PRPF6 promotes androgen receptor/androgen receptor-variant 7 actions in castration-resistant prostate cancer cells.
Title: PRPF6 promotes androgen receptor/androgen receptor-variant 7 actions in castration-resistant prostate cancer cells.
Splicing factor PRPF6 upregulates oncogenic androgen receptor signaling pathway in hepatocellular carcinoma.
Title: Splicing factor PRPF6 upregulates oncogenic androgen receptor signaling pathway in hepatocellular carcinoma.
an essential role for PRPF6 in cancer via splicing of distinct growth-related gene products.
Title: An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth.
Our results identify PRPF6 as the sixth gene involved in pre-mRNA splicing and dominant RP, corroborating the hypothesis that deficiencies in the spliceosome play an important role in the molecular pathology of this disease.
Title: A missense mutation in PRPF6 causes impairment of pre-mRNA splicing and autosomal-dominant retinitis pigmentosa.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
The authors provide evidence that PRP6 and PRP31 are directly phosphorylated by human PRP4 kinase (PRP4K) concomitant with their incorporation into B complexes.
Title: Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation.
C20orf14 may have a role in progression of lymphoma
Title: The expression and bioinformatic analysis of a novel gene C20orf14 associated with lymphoma.
The interaction of CD2BP2 with a tri-snRNP bridging protein (Prp6), coupled with CD2BP2's absence from the tri-snRNP, suggests it might function in tri-snRNP assembly
Title: The human U5 snRNP 52K protein (CD2BP2) interacts with U5-102K (hPrp6), a U4/U6.U5 tri-snRNP bridging protein, but dissociates upon tri-snRNP formation.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Retinitis pigmentosa 60 MedGen: C3151434 OMIM: 613983 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	not available

EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae, PRPF6) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, pre-mRNA processing factor 6 homolog (PRPF6), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with PRPF6 is increased by RRE	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay 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
enables protein-macromolecule adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables ribonucleoprotein complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA splicing	NAS Non-traceable Author Statement more info	PubMed
involved_in RNA splicing, via transesterification reactions	NAS Non-traceable Author Statement more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator more info	PubMed
involved_in mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA splicing, via spliceosome	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in spliceosomal complex assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in spliceosomal tri-snRNP complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal tri-snRNP complex assembly	IC Inferred by Curator more info	PubMed
involved_in spliceosomal tri-snRNP complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in spliceosomal tri-snRNP complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of U2-type precatalytic spliceosome	IDA Inferred from Direct Assay more info	PubMed
part_of U4/U6 x U5 tri-snRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U4/U6 x U5 tri-snRNP complex	IDA Inferred from Direct Assay more info	PubMed
part_of U4/U6 x U5 tri-snRNP complex	IPI Inferred from Physical Interaction more info	PubMed
part_of U5 snRNP	IDA Inferred from Direct Assay more info	PubMed
part_of catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of spliceosomal complex	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: pre-mRNA-processing factor 6

Names: PRP6 homolog; PRP6 pre-mRNA processing factor 6 homolog; U5 snRNP-associated 102 kDa protein; U5-102 kDa protein; androgen receptor N-terminal domain transactivating protein-1; p102 U5 small nuclear ribonucleoprotein particle-binding protein; putative mitochondrial outer membrane protein import receptor

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_029719.1 RefSeqGene

Range

5055..57023

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_012469.4 → NP_036601.2 pre-mRNA-processing factor 6

See identical proteins and their annotated locations for NP_036601.2

Status: REVIEWED

Source sequence(s)

AF221842, BP366197

Consensus CDS

CCDS13550.1

UniProtKB/Swiss-Prot

B2RAR5, B3KMC6, O94906, O95109, Q5VXS5, Q9H3Z1, Q9H4T9, Q9H4U8, Q9NTE6

Related

ENSP00000266079.4, ENST00000266079.5

Conserved Domains (3) summary

TIGR02917
Location:290 → 846

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:708 → 738

TPR; TPR repeat [structural motif]

pfam06424
Location:13 → 169

PRP1_N; PRP1 splicing factor, N-terminal

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_000020.11 Reference GRCh38.p14 Primary Assembly

Range

63981132..64033100

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006723769.4 → XP_006723832.1 pre-mRNA-processing factor 6 isoform X1

Conserved Domains (3) summary

sd00006
Location:635 → 665

TPR; TPR repeat [structural motif]

pfam06424
Location:13 → 169

PRP1_N; PRP1 splicing factor, N-terminal

cl26002
Location:289 → 773

TPR_11; TPR repeat