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Aliases for PRPF40A Gene

Aliases for PRPF40A Gene

  • Pre-MRNA Processing Factor 40 Homolog A 2 3 5
  • PRP40 Pre-MRNA Processing Factor 40 Homolog A 2 3
  • Huntingtin-Interacting Protein 10 3 4
  • Renal Carcinoma Antigen NY-REN-6 3 4
  • Huntingtin-Interacting Protein A 3 4
  • Fas Ligand-Associated Factor 1 3 4
  • Huntingtin Yeast Partner A 3 4
  • Formin-Binding Protein 11 3 4
  • Formin-Binding Protein 3 2 4
  • Formin Binding Protein 3 2 3
  • HIP-10 3 4
  • FNBP3 3 4
  • FBP11 3 4
  • FLAF1 3 4
  • HIP10 3 4
  • HYPA 3 4
  • PRP40 Pre-MRNA Processing Factor 40 Homolog A (S. Cerevisiae) 2
  • PRP40 Pre-MRNA Processing Factor 40 Homolog A (Yeast) 2
  • Pre-MRNA-Processing Factor 40 Homolog A 3
  • Fas-Ligand Associated Factor 1 3
  • NY-REN-6 Antigen 3
  • NY-REN-6 3
  • FBP-11 3
  • Prp40 3

External Ids for PRPF40A Gene

Previous HGNC Symbols for PRPF40A Gene

  • FNBP3

Previous GeneCards Identifiers for PRPF40A Gene

  • GC02M153338
  • GC02M153216
  • GC02M153508
  • GC02M145394

Summaries for PRPF40A Gene

GeneCards Summary for PRPF40A Gene

PRPF40A (Pre-MRNA Processing Factor 40 Homolog A) is a Protein Coding gene. Diseases associated with PRPF40A include Rett Syndrome. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and proline-rich region binding. An important paralog of this gene is PRPF40B.

UniProtKB/Swiss-Prot for PRPF40A Gene

  • Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis. May be involved in pre-mRNA splicing.

Gene Wiki entry for PRPF40A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF40A Gene

Genomics for PRPF40A Gene

Regulatory Elements for PRPF40A Gene

Enhancers for PRPF40A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G152715 1.2 ENCODE 11.2 +0.1 89 4.3 CREB3L1 AGO1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 SSRP1 PRPF40A ARL6IP6
GH02G152694 0.9 Ensembl ENCODE 11 +23.5 23531 1.6 IRF2 BHLHE40 CHD1 SIN3A ATF2 STAT2 FOS IRF1 MLLT1 PRPF40A ARL6IP6 GC02M152671
GH02G152730 1 Ensembl ENCODE 9.2 -12.9 -12904 1.0 SOX13 FOXA2 MAX CEBPG BMI1 RAD21 MTA3 CTBP1 GATA3 RCOR1 PRPF40A ARL6IP6 GC02P152749
GH02G152646 1.1 Ensembl ENCODE dbSUPER 5.7 +70.8 70777 1.7 JUND MAFF ZNF316 CHD1 HNF4A EMSY MAFK STAM2 PRPF40A LOC105373690 GC02M152671
GH02G152611 1.3 Ensembl ENCODE dbSUPER 4.8 +105.7 105697 1.8 CTCF BACH1 CEBPG RAD21 RELA FOSL1 EED ETV6 RELB FOS PRPF40A GC02M152586 GC02M152585 LOC105373690
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PRPF40A on UCSC Golden Path with GeneCards custom track

Promoters for PRPF40A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000124796 -3 4001 CREB3L1 AGO1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 SSRP1

Genomic Location for PRPF40A Gene

Chromosome:
2
Start:
152,651,593 bp from pter
End:
152,717,997 bp from pter
Size:
66,405 bases
Orientation:
Minus strand

Genomic View for PRPF40A Gene

Genes around PRPF40A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF40A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRPF40A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF40A Gene

Proteins for PRPF40A Gene

  • Protein details for PRPF40A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75400-PR40A_HUMAN
    Recommended name:
    Pre-mRNA-processing factor 40 homolog A
    Protein Accession:
    O75400
    Secondary Accessions:
    • O43856
    • O75404
    • Q8TBQ1
    • Q9H782
    • Q9NWU9
    • Q9P0Q2
    • Q9Y5A8

    Protein attributes for PRPF40A Gene

    Size:
    957 amino acids
    Molecular mass:
    108805 Da
    Quaternary structure:
    • Interacts with the N-terminus of HTT. Interacts with the phosphorylated C-terminal domain of POLR2A. Interacts with AKAP8L, SF1, SRPK1, CARD8, ATBF1 and MECP2 (By similarity). Interacts through the WW domains with formin proline-rich regions and with WASL/N-WASP (By similarity).
    SequenceCaution:
    • Sequence=AAC27501.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAC27502.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAC27506.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAD42862.1; Type=Frameshift; Positions=953; Evidence={ECO:0000305}; Sequence=AAF36145.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=AAH11788.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence starting in position 409.; Evidence={ECO:0000305}; Sequence=BAA91277.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15016.1; Type=Miscellaneous discrepancy; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRPF40A Gene

    Alternative splice isoforms for PRPF40A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRPF40A Gene

Post-translational modifications for PRPF40A Gene

  • Ubiquitination at Lys196, isoforms=2, 3718, and Lys727
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PRPF40A Gene

Domains & Families for PRPF40A Gene

Protein Domains for PRPF40A Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

O75400

UniProtKB/Swiss-Prot:

PR40A_HUMAN :
  • The WW domains are essential for localization to nuclear speckles.
  • Belongs to the PRPF40 family.
Domain:
  • The WW domains are essential for localization to nuclear speckles.
Family:
  • Belongs to the PRPF40 family.
genes like me logo Genes that share domains with PRPF40A: view

No data available for Gene Families for PRPF40A Gene

Function for PRPF40A Gene

Molecular function for PRPF40A Gene

UniProtKB/Swiss-Prot Function:
Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby inhibiting its cytoplasmic function (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. May play a role in cytokinesis. May be involved in pre-mRNA splicing.

Gene Ontology (GO) - Molecular Function for PRPF40A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22681889
GO:0005515 protein binding IPI 15383276
GO:0070064 proline-rich region binding IEA --
genes like me logo Genes that share ontologies with PRPF40A: view
genes like me logo Genes that share phenotypes with PRPF40A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRPF40A Gene

Localization for PRPF40A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF40A Gene

Nucleus speckle. Nucleus matrix. Note=Colocalizes with AKAP8L in the nuclear matrix. {ECO:0000250}.

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 PRPF40A gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PRPF40A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005685 U1 snRNP IBA --
GO:0005829 cytosol IDA --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with PRPF40A: view

Pathways & Interactions for PRPF40A Gene

genes like me logo Genes that share pathways with PRPF40A: view

Pathways by source for PRPF40A Gene

1 BioSystems pathway for PRPF40A Gene
1 KEGG pathway for PRPF40A Gene

Gene Ontology (GO) - Biological Process for PRPF40A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0007010 cytoskeleton organization IMP 21834987
GO:0007049 cell cycle IEA --
GO:0008360 regulation of cell shape IMP 21834987
genes like me logo Genes that share ontologies with PRPF40A: view

No data available for SIGNOR curated interactions for PRPF40A Gene

Drugs & Compounds for PRPF40A Gene

No Compound Related Data Available

Transcripts for PRPF40A Gene

Unigene Clusters for PRPF40A Gene

PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF40A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20
SP1:
SP2:
SP3:
SP4: - - -
SP5: - -
SP6: - -
SP7:

Relevant External Links for PRPF40A Gene

GeneLoc Exon Structure for
PRPF40A
ECgene alternative splicing isoforms for
PRPF40A

Expression for PRPF40A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRPF40A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRPF40A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PRPF40A Gene



Protein tissue co-expression partners for PRPF40A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF40A Gene:

PRPF40A

SOURCE GeneReport for Unigene cluster for PRPF40A Gene:

Hs.643580

mRNA Expression by UniProt/SwissProt for PRPF40A Gene:

O75400-PR40A_HUMAN
Tissue specificity: Expressed in the brain cortex (at protein level). Widely expressed.

Evidence on tissue expression from TISSUES for PRPF40A Gene

  • Nervous system(4.6)
  • Liver(4.4)
  • Blood(4.3)
  • Muscle(4.3)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with PRPF40A: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF40A Gene

Orthologs for PRPF40A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF40A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRPF40A 34 35
  • 99.78 (n)
cow
(Bos Taurus)
Mammalia PRPF40A 34 35
  • 94.58 (n)
dog
(Canis familiaris)
Mammalia PRPF40A 34 35
  • 93.91 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PRPF40A 35
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prpf40a 34 16 35
  • 91.44 (n)
rat
(Rattus norvegicus)
Mammalia Prpf40a 34
  • 91.36 (n)
oppossum
(Monodelphis domestica)
Mammalia PRPF40A 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRPF40A 34 35
  • 80.02 (n)
lizard
(Anolis carolinensis)
Reptilia PRPF40A 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf40a 34
  • 70.45 (n)
Str.8902 34
zebrafish
(Danio rerio)
Actinopterygii prpf40a 34 35
  • 68.65 (n)
fnbp3 34
fruit fly
(Drosophila melanogaster)
Insecta CG3542 35
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ZK1098.1 34 35
  • 52.21 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP40 35
  • 27 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons PRP40B 34
  • 45.37 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11107 35
  • 47 (a)
OneToMany
Species where no ortholog for PRPF40A 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)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PRPF40A Gene

ENSEMBL:
Gene Tree for PRPF40A (if available)
TreeFam:
Gene Tree for PRPF40A (if available)

Paralogs for PRPF40A Gene

Paralogs for PRPF40A Gene

(2) SIMAP similar genes for PRPF40A Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with PRPF40A: view

Variants for PRPF40A Gene

Sequence variations from dbSNP and Humsavar for PRPF40A Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs867616255 Uncertain significance 152,718,816(+) GCGTG(A/G)TCAGA intron-variant, nc-transcript-variant, upstream-variant-2KB, reference, stop-gained
rs1000008360 -- 152,715,675(+) ATTGG(C/T)ATTCT intron-variant
rs1000159347 -- 152,678,131(+) AATAA(C/T)ACAAG intron-variant
rs1000227085 -- 152,688,291(+) TGCAC(C/T)TGGCC intron-variant
rs1000313612 -- 152,684,241(+) TCACT(A/C)TCATG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PRPF40A Gene

Variant ID Type Subtype PubMed ID
esv34659 CNV loss 17911159
esv3592922 CNV loss 21293372
nsv7331 OTHER inversion 18451855
nsv834420 CNV loss 17160897
nsv834421 CNV loss 17160897

Variation tolerance for PRPF40A Gene

Residual Variation Intolerance Score: 3.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 15.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PRPF40A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRPF40A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRPF40A Gene

Disorders for PRPF40A Gene

MalaCards: The human disease database

(1) MalaCards diseases for PRPF40A Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
rett syndrome
  • rett syndrome, preserved speech variant
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PRPF40A

Genetic Association Database (GAD)
PRPF40A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRPF40A
genes like me logo Genes that share disorders with PRPF40A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRPF40A Gene

Publications for PRPF40A Gene

  1. Interaction of the nuclear matrix protein NAKAP with HypA and huntingtin: implications for nuclear toxicity in Huntington's disease pathogenesis. (PMID: 16391387) Sayer J.A. … Coghlan V.M. (NeuroMolecular Med. 2005) 3 4 22 64
  2. Huntingtin interacts with a family of WW domain proteins. (PMID: 9700202) Faber P.W. … MacDonald M.E. (Hum. Mol. Genet. 1998) 3 4 22 64
  3. Identification and characterization of a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. (PMID: 21834987) Bai S.W. … Ridley A.J. (BMC Biol. 2011) 3 4 64
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier L.W. … Wilson R.K. (Nature 2005) 3 4 64

Products for PRPF40A Gene

Sources for PRPF40A Gene

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