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Aliases for RP9 Gene

Aliases for RP9 Gene

  • RP9, Pre-MRNA Splicing Factor 2 3 5
  • Retinitis Pigmentosa 9 (Autosomal Dominant) 2 3
  • Pim-1 Kinase Associated Protein 2 3
  • Pim-1-Associated Protein 3 4
  • PAP-1 3 4
  • Retinitis Pigmentosa 9 Protein 3
  • PAP1 3

External Ids for RP9 Gene

Previous GeneCards Identifiers for RP9 Gene

  • GC07U990086
  • GC07M032877
  • GC07M032907
  • GC07M033100
  • GC07M033013

Summaries for RP9 Gene

Entrez Gene Summary for RP9 Gene

  • 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]

GeneCards Summary for RP9 Gene

RP9 (RP9, Pre-MRNA Splicing Factor) is a Protein Coding gene. Diseases associated with RP9 include Retinitis Pigmentosa 9 and Retinitis Pigmentosa. Among its related pathways are mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding.

UniProtKB/Swiss-Prot for RP9 Gene

  • Is thought to be a target protein for the PIM1 kinase. May play some roles in B-cell proliferation in association with PIM1 (By similarity).

Gene Wiki entry for RP9 Gene

Additional gene information for RP9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RP9 Gene

Genomics for RP9 Gene

GeneHancer (GH) Regulatory Elements for RP9 Gene

Promoters and enhancers for RP9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J033107 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 657.1 +0.8 764 3.1 PKNOX1 ATF1 ARNT ZFP64 ARID4B SIN3A ZNF2 ZNF48 YY1 ETS1 RP9 BBS9 RP9P PIR62751
GH07J032956 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 8.1 +151.6 151584 2.7 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF263 SP3 SP5 SMARCB1 FKBP9 RP9P KBTBD2 NT5C3A RP9 RNU6-388P
GH07J032489 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 6.8 +618.9 618862 2.4 ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D LSM5 LOC100130673 DPY19L1P1 ENSG00000273014 RP9 SLC25A5P5 GC07P032460
GH07J033038 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 5.7 +67.6 67622 7.4 ATF1 FOXA2 ARNT ARID4B SIN3A YY1 TCF12 ATF7 RUNX3 RXRA KBTBD2 NT5C3A FKBP9 RP9P RP9 GC07M033036 RN7SL505P
GH07J032505 Enhancer 1.1 Ensembl ENCODE 10.3 +602.4 602398 2.6 PKNOX1 SMAD1 ATF1 ARNT YY1 TCF12 ZNF766 GATA2 FOS ATF7 LOC100130673 DPY19L1P1 RP9 RP9P SLC25A5P5 AVL9 GC07P032460 PIR53283
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RP9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RP9 gene promoter:
  • CUTL1
  • FOXC1
  • MRF-2
  • c-Myb
  • GCNF
  • GCNF-1
  • GCNF-2

Genomic Locations for RP9 Gene

Genomic Locations for RP9 Gene
14,605 bases
Minus strand
14,605 bases
Minus strand

Genomic View for RP9 Gene

Genes around RP9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RP9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RP9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RP9 Gene

Proteins for RP9 Gene

  • Protein details for RP9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Retinitis pigmentosa 9 protein
    Protein Accession:

    Protein attributes for RP9 Gene

    221 amino acids
    Molecular mass:
    26107 Da
    Quaternary structure:
    • Binds to PIM1 (By similarity). Binds to ZNHIT4.

neXtProt entry for RP9 Gene

Post-translational modifications for RP9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RP9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RP9 Gene

Domains & Families for RP9 Gene

Gene Families for RP9 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RP9 Gene


Suggested Antigen Peptide Sequences for RP9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RP9: view

No data available for UniProtKB/Swiss-Prot for RP9 Gene

Function for RP9 Gene

Molecular function for RP9 Gene

UniProtKB/Swiss-Prot Function:
Is thought to be a target protein for the PIM1 kinase. May play some roles in B-cell proliferation in association with PIM1 (By similarity).

Gene Ontology (GO) - Molecular Function for RP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0005515 protein binding IPI 15652350
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RP9: view
genes like me logo Genes that share phenotypes with RP9: view

Human Phenotype Ontology for RP9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RP9 Gene

Localization for RP9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RP9 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RP9 gene
Compartment Confidence
nucleus 5
cytosol 5
endoplasmic reticulum 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005785 signal recognition particle receptor complex IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with RP9: view

Pathways & Interactions for RP9 Gene

SuperPathway Contained pathways
1 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with RP9: view

Pathways by source for RP9 Gene

1 KEGG pathway for RP9 Gene

Gene Ontology (GO) - Biological Process for RP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008380 RNA splicing IEA,TAS 15652350
GO:0050890 cognition IMP 23227193
genes like me logo Genes that share ontologies with RP9: view

No data available for SIGNOR curated interactions for RP9 Gene

Drugs & Compounds for RP9 Gene

(1) Drugs for RP9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with RP9: view

Transcripts for RP9 Gene

mRNA/cDNA for RP9 Gene

(2) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(210) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RP9 Gene

Retinitis pigmentosa 9 (autosomal dominant):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RP9 Gene

No ASD Table

Relevant External Links for RP9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RP9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RP9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RP9 Gene

This gene is overexpressed in Fetal testis (19.4), CD4 Tcells (14.8), Fetal Liver (13.2), CD8 Tcells (11.5), and Fetal heart (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RP9 Gene

Protein tissue co-expression partners for RP9 Gene

NURSA nuclear receptor signaling pathways regulating expression of RP9 Gene:


SOURCE GeneReport for Unigene cluster for RP9 Gene:


mRNA Expression by UniProt/SwissProt for RP9 Gene:

Tissue specificity: Appears to be expressed in a wide range of tissues.

Evidence on tissue expression from TISSUES for RP9 Gene

  • Muscle(4.3)
  • Spleen(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RP9 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with RP9: view

No data available for mRNA differential expression in normal tissues for RP9 Gene

Orthologs for RP9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RP9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RP9 34 33
  • 99.25 (n)
(Canis familiaris)
Mammalia RP9 34 33
  • 92.57 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 92 (a)
-- 34
  • 88 (a)
-- 34
  • 88 (a)
-- 34
  • 84 (a)
(Bos Taurus)
Mammalia RP9 34 33
  • 91.31 (n)
(Mus musculus)
Mammalia Rp9 16 34 33
  • 88.39 (n)
(Rattus norvegicus)
Mammalia Rp9 33
  • 88.14 (n)
(Ornithorhynchus anatinus)
Mammalia RP9 34
  • 55 (a)
(Gallus gallus)
Aves RP9 34
  • 67 (a)
(Anolis carolinensis)
Reptilia RP9 34
  • 68 (a)
(Danio rerio)
Actinopterygii rp9 34
  • 64 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
Species where no ortholog for RP9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RP9 Gene

Gene Tree for RP9 (if available)
Gene Tree for RP9 (if available)
Evolutionary constrained regions (ECRs) for RP9: view image

Paralogs for RP9 Gene Pseudogenes for RP9 Gene

genes like me logo Genes that share paralogs with RP9: view

No data available for Paralogs for RP9 Gene

Variants for RP9 Gene

Sequence variations from dbSNP and Humsavar for RP9 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs104894037 uncertain-significance, Retinitis pigmentosa 9, Retinitis pigmentosa 9 (RP9) [MIM:180104] 33,096,550(-) T/A coding_sequence_variant, missense_variant
rs104894039 pathogenic, Retinitis pigmentosa 9, Retinitis pigmentosa 9 (RP9) [MIM:180104] 33,095,391(-) T/C coding_sequence_variant, missense_variant
rs115938195 likely-benign, Retinitis Pigmentosa, Dominant 33,100,558(-) G/A coding_sequence_variant, synonymous_variant
rs150987618 benign, likely-benign, not specified, Retinitis Pigmentosa, Dominant 33,095,271(-) T/C coding_sequence_variant, missense_variant
rs369792814 uncertain-significance, Retinitis Pigmentosa, Dominant 33,095,159(-) G/A 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for RP9 Gene

Variant ID Type Subtype PubMed ID
dgv1080e201 CNV deletion 23290073
dgv11272n54 CNV gain 21841781
dgv1278e214 CNV gain 21293372
dgv1880e212 CNV gain 25503493
dgv6319n100 CNV gain 25217958
dgv808n27 CNV gain 19166990
esv2761318 CNV gain 21179565
esv3612750 OTHER inversion 21293372
nsv1029220 CNV gain 25217958
nsv1135982 CNV deletion 24896259
nsv436907 CNV insertion 17901297
nsv508450 CNV deletion 20534489
nsv520406 CNV gain 19592680
nsv830942 CNV gain 17160897

Variation tolerance for RP9 Gene

Residual Variation Intolerance Score: 56.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.61; 82.65% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RP9 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RP9 Gene

Disorders for RP9 Gene

MalaCards: The human disease database

(12) MalaCards diseases for RP9 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search RP9 in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 9 (RP9) [MIM:180104]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:12032732}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RP9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RP9: view

No data available for Genatlas for RP9 Gene

Publications for RP9 Gene

  1. A novel nucleolar protein, PAPA-1, induces growth arrest as a result of cell cycle arrest at the G1 phase. (PMID: 15556297) Kuroda TS … Iguchi-Ariga SM (Gene 2004) 3 4 22 58
  2. PAP-1, the mutated gene underlying the RP9 form of dominant retinitis pigmentosa, is a splicing factor. (PMID: 15474994) Maita H … Iguchi-Ariga SM (Experimental cell research 2004) 2 3 22 58
  3. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 44 58
  4. CIR, a corepressor of CBF1, binds to PAP-1 and effects alternative splicing. (PMID: 15652350) Maita H … Iguchi-Ariga SM (Experimental cell research 2005) 3 22 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for RP9 Gene

Sources for RP9 Gene

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