RP9 RP9 pre-mRNA splicing factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: RP9provided by HGNC
Official Full Name: RP9 pre-mRNA splicing factorprovided by HGNC
Primary source: HGNC:HGNC:10288
See related: Ensembl:ENSG00000164610 MIM:607331; AllianceGenome:HGNC:10288
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: PAP1; PAP-1
Summary: The protein encoded by this gene can be bound and phosphorylated by the protooncogene PIM1 product, a serine/threonine protein kinase . This protein localizes in nuclear speckles containing the splicing factors, and has a role in pre-mRNA splicing. CBF1-interacting protein (CIR), a corepressor of CBF1, can also bind to this protein and effects alternative splicing. Mutations in this gene result in autosomal dominant retinitis pigmentosa-9. This gene has a pseudogene (GeneID: 441212), which is located in tandem array approximately 166 kb distal to this gene. [provided by RefSeq, Sep 2009]
Expression: Ubiquitous expression in testis (RPKM 5.1), adrenal (RPKM 4.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p14.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (33094797..33109404, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (33234370..33248976, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (33134409..33149016, complement)

Chromosome 7 - NC_000007.14 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?

Observational study of genetic testing. (HuGE Navigator)
Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
CIR was found to be colocalized with PAP-1 in nuclear speckles.
Title: CIR, a corepressor of CBF1, binds to PAP-1 and effects alternative splicing.
Mutations in a protein target of the Pim-1 kinase associated with the RP9 form of autosomal dominant retinitis pigmentosa
Title: Mutations in a protein target of the Pim-1 kinase associated with the RP9 form of autosomal dominant retinitis pigmentosa.
Has a role in pre-mRNA splicing, further evidence that PAP-1 is indeed the RP9 gene.
Title: PAP-1, the mutated gene underlying the RP9 form of dominant retinitis pigmentosa, is a splicing factor.
PAP-1 interacted with Prp3p but not Prp31p in human cells and yeast, and the basic region of PAP-1 and the C-terminal region of Prp3p, regions beside spots found in retinitis pigmentosa mutations, were needed for binding
Title: Association of PAP-1 and Prp3p, the products of causative genes of dominant retinitis pigmentosa, in the tri-snRNP complex.

Submit: New GeneRIF Correction

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
Retinitis pigmentosa 9 MedGen: C1867300 OMIM: 180104 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs

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

D7S460 (e-PCR), detects polymorphism
- UniSTS:5447

RH65893 (e-PCR)
- UniSTS:338

SGC33228 (e-PCR)
- UniSTS:2400

RH44672 (e-PCR)
- UniSTS:20929

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	TAS Traceable Author Statement more info	PubMed
involved_in cognition	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of signal recognition particle receptor complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: retinitis pigmentosa 9 protein

Names: Pim-1 kinase associated protein; pim-1-associated protein; retinitis pigmentosa 9 (autosomal dominant)

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.