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... See more...

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
  • Retinitis Pigmentosa 9 Protein 3 4
  • Pim-1-Associated Protein 3 4
  • PAP-1 3 4
  • PAP1 3

External Ids for RP9 Gene

Previous GeneCards Identifiers for RP9 Gene

  • GC07U990086
  • GC07M032877
  • GC07M032907
  • GC07M033100
  • GC07M033013
  • GC07M033134

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 Summary 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 , Rfam classification 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
Score
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 CraniofacialAtlas 507 +0.6 566 3.5 HNRNPK CTCF POLR2G USF1 PHF8 JUND ZFX POLR2A ZBTB26 REST RP9 BBS9 RF00017-6108 lnc-BBS9-2 lnc-NT5C3A-1 FKBP9 RP9P piR-39706-002
GH07J032956 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 8.1 +151.7 151703 3 NRF1 TCF12 USF1 POLR2G GTF2E2 PHF8 TEAD4 ZFX ZIC2 POLR2A FKBP9 lnc-NT5C3A-3 RP9P KBTBD2 NT5C3A RP9
GH07J032489 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 6.8 +619.0 619043 2.7 ZBTB40 ZNF217 EP300 CTCF SIN3A NRF1 TCF12 POLR2G SP1 NCOR1 LSM5 lnc-PDE1C-2 ENSG00000226468 DPY19L1P1 ENSG00000273014 RP9 HSALNG0057079
GH07J032940 Promoter/Enhancer 1.6 Ensembl ENCODE CraniofacialAtlas 8.2 +167.3 167255 3.5 HNRNPK CTCF NRF1 POLR2G PHF8 ZFX ZBTB10 ZBTB26 REST KLF4 RP9P lnc-KBTBD2-2 KBTBD2 RP9 FKBP9 piR-38580-310
GH07J032505 Enhancer 0.9 ENCODE 10.3 +602.4 602401 2.6 GTF2E2 JUND FOS AFF1 TARDBP MYC CTBP1 JUN NFRKB HINFP ENSG00000226468 DPY19L1P1 RP9 RP9P SLC25A5P5 AVL9 L13714-413
- 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RP9

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

Genomic Locations for RP9 Gene

Genomic Locations for RP9 Gene
chr7:33,094,797-33,109,404
(GRCh38/hg38)
Size:
14,608 bases
Orientation:
Minus strand
chr7:33,134,409-33,149,013
(GRCh37/hg19)
Size:
14,605 bases
Orientation:
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:
    Q8TA86-RP9_HUMAN
    Recommended name:
    Retinitis pigmentosa 9 protein
    Protein Accession:
    Q8TA86

    Protein attributes for RP9 Gene

    Size:
    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

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RP9 Gene

GenScript: Design optimal peptide antigens:
  • Pim-1-associated protein (RP9_HUMAN)
genes like me logo Genes that share domains with RP9: view

No data available for Graphical View of Domain Structure and 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).

Phenotypes From GWAS Catalog for RP9 Gene

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: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 Models for RP9 Gene

MGI Knock Outs for RP9:
  • Rp9 Rp9<tm1b(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for RP9 Gene

Localization for RP9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RP9 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
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
endoplasmic reticulum 3
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleoplasm (4)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RP9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA --
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

PathCards logo

SuperPathways 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 TAS,IEA 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

1 REFSEQ mRNAs :
1 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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
RP9

Expression for RP9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RP9

SOURCE GeneReport for Unigene cluster for RP9 Gene:

Hs.326805

mRNA Expression by UniProt/SwissProt for RP9 Gene:

Q8TA86-RP9_HUMAN
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
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
Pelvis:
  • penis
  • testicle
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia RP9 31 30
  • 99.25 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RP9 31 30
  • 92.57 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 88 (a)
OneToMany
-- 31
  • 88 (a)
OneToMany
-- 31
  • 84 (a)
OneToMany
cow
(Bos Taurus)
Mammalia RP9 31 30
  • 91.31 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rp9 17 31 30
  • 88.39 (n)
rat
(Rattus norvegicus)
Mammalia Rp9 30
  • 88.14 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RP9 31
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves RP9 31
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RP9 31
  • 68 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii rp9 31
  • 64 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 55 (a)
OneToOne
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

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

Paralogs for RP9 Gene

Pseudogenes.org 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RP9 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
795939 Likely Benign: not provided 33,095,268(-) G/C MISSENSE_VARIANT
rs1010772189 Uncertain Significance: not provided 33,109,368(-) G/A MISSENSE_VARIANT
rs104894037 Uncertain Significance: Retinitis pigmentosa 9. Retinitis pigmentosa 9 (RP9) [MIM:180104] 33,096,550(-) T/Ap.His137Leu MISSENSE_VARIANT
rs104894039 Pathogenic: Retinitis pigmentosa 9. Retinitis pigmentosa 9 (RP9) [MIM:180104] 33,095,391(-) T/Cp.Asp170Gly MISSENSE_VARIANT
rs114747263 Benign/Likely Benign: not specified; not provided 33,099,404(-) T/C SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for RP9 Gene

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)
RP9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RP9

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

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

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

UniProtKB/Swiss-Prot

RP9_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 23 54
  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 23 54
  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 41 54
  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 23 54
  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 54

Products for RP9 Gene

Sources for RP9 Gene