Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PRPF40B Gene

Aliases for PRPF40B Gene

  • Pre-MRNA Processing Factor 40 Homolog B 2 3 5
  • Huntingtin Interacting Protein C 2 3
  • Huntingtin Yeast Partner C 3 4
  • HYPC 3 4
  • PRP40 Pre-MRNA Processing Factor 40 Homolog B (S. Cerevisiae) 2
  • PRP40 Pre-MRNA Processing Factor 40 Homolog B (Yeast) 2
  • PRP40 Pre-MRNA Processing Factor 40 Homolog B 3
  • PRP40 Homolog, Pre-MRNA Processing Factor B 2
  • Pre-MRNA-Processing Factor 40 Homolog B 3
  • Huntingtin-Interacting Protein C 4

External Ids for PRPF40B Gene

Previous GeneCards Identifiers for PRPF40B Gene

  • GC12P048304
  • GC12P050017
  • GC12P047049
  • GC12P049963

Summaries for PRPF40B Gene

Entrez Gene Summary for PRPF40B Gene

  • This gene encodes a WW-domain containing protein similar to yeast splicing factor PRP40. This protein has been shown to interact with Huntingtin and methyl CpG binding protein 2 (MeCP2). Alternative splicing results in different transcript variants. [provided by RefSeq, Aug 2014]

GeneCards Summary for PRPF40B Gene

PRPF40B (Pre-MRNA Processing Factor 40 Homolog B) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway. An important paralog of this gene is PRPF40A.

UniProtKB/Swiss-Prot for PRPF40B Gene

  • May be involved in pre-mRNA splicing.

Additional gene information for PRPF40B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF40B Gene

Genomics for PRPF40B Gene

GeneHancer (GH) Regulatory Elements for PRPF40B Gene

Promoters and enhancers for PRPF40B 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
GH12I049621 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 550.2 +55.5 55484 3.6 PKNOX1 CLOCK MLX ARID4B SIN3A IRF4 YY1 POLR2B ZNF143 FOS PRPF40B FMNL3 RNU6-834P TMBIM6 MCRS1 C1QL4 HIGD1AP9 PIR31660
GH12I049564 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 561.3 -1.4 -1385 5.1 PKNOX1 CLOCK SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 PRPF40B MCRS1 ENSG00000257298 ADCY6 LOC100422296 SMARCD1 KMT2D TUBA1C SPATS2 GC12M049547
GH12I048865 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 89.1 -702.0 -701988 2.2 HDGF PKNOX1 FOXA2 ZFP64 ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 RND1 DDX23 KMT2D KANSL2 LOC390314 CCNT1 LMBR1L SENP1 BCDIN3D PRPF40B
GH12I049129 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 64.3 -436.9 -436851 4.6 CLOCK MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ENSG00000200309 GC12M049133 TUBA1B DDX23 LMBR1L KMT2D SMARCD1 LOC390314 BCDIN3D CCNT1
GH12I050399 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 49.9 +833.7 833665 4 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF548 SP3 ZNF610 ZNF585B NBN GC12M050402 LARP4 LIMA1 SMARCD1 PRPF40B BCDIN3D ATF1 LOC100422296 ENSG00000257298 ENSG00000257964
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRPF40B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRPF40B gene promoter:

Genomic Locations for PRPF40B Gene

Genomic Locations for PRPF40B Gene
76,452 bases
Plus strand

Genomic View for PRPF40B Gene

Genes around PRPF40B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF40B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRPF40B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF40B Gene

Proteins for PRPF40B Gene

  • Protein details for PRPF40B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pre-mRNA-processing factor 40 homolog B
    Protein Accession:
    Secondary Accessions:
    • O75401
    • Q6PI09
    • Q6ZWB3
    • Q8NCZ1
    • Q9H5G4
    • Q9NT95

    Protein attributes for PRPF40B Gene

    871 amino acids
    Molecular mass:
    99358 Da
    Quaternary structure:
    • Interacts with the N-terminus of HD.
    • Sequence=AAH50398.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAB15662.1; Type=Frameshift; Positions=537, 851; Evidence={ECO:0000305};

    Alternative splice isoforms for PRPF40B Gene


neXtProt entry for PRPF40B Gene

Post-translational modifications for PRPF40B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRPF40B Gene

Domains & Families for PRPF40B Gene

Gene Families for PRPF40B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PRPF40B Gene

Suggested Antigen Peptide Sequences for PRPF40B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PRPF40 family.
  • Belongs to the PRPF40 family.
genes like me logo Genes that share domains with PRPF40B: view

Function for PRPF40B Gene

Molecular function for PRPF40B Gene

UniProtKB/Swiss-Prot Function:
May be involved in pre-mRNA splicing.

Phenotypes From GWAS Catalog for PRPF40B Gene

Gene Ontology (GO) - Molecular Function for PRPF40B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA --
genes like me logo Genes that share ontologies with PRPF40B: view
genes like me logo Genes that share phenotypes with PRPF40B: view

Animal Model Products

CRISPR Products

miRNA for PRPF40B Gene

miRTarBase miRNAs that target PRPF40B

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRPF40B Gene

Localization for PRPF40B Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF40B Gene

Nucleus speckle.

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 PRPF40B gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
endoplasmic reticulum 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Aggresome (2)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRPF40B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005685 U1 snRNP IBA --
GO:0016607 nuclear speck IEA --
GO:0071004 U2-type prespliceosome IBA --
genes like me logo Genes that share ontologies with PRPF40B: view

Pathways & Interactions for PRPF40B Gene

SuperPathways for PRPF40B Gene

SuperPathway Contained pathways
1 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with PRPF40B: view

Pathways by source for PRPF40B Gene

1 KEGG pathway for PRPF40B Gene

Gene Ontology (GO) - Biological Process for PRPF40B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IBA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with PRPF40B: view

No data available for SIGNOR curated interactions for PRPF40B Gene

Drugs & Compounds for PRPF40B Gene

No Compound Related Data Available

Transcripts for PRPF40B Gene

Unigene Clusters for PRPF40B Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF40B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b · 17c ^
SP2: -
SP6: -
SP7: -

ExUns: 18 ^ 19 ^ 20a · 20b

Relevant External Links for PRPF40B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRPF40B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRPF40B Gene

Protein differential expression in normal tissues from HIPED for PRPF40B Gene

This gene is overexpressed in Heart (38.3), Retina (14.2), and Testis (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PRPF40B Gene

Protein tissue co-expression partners for PRPF40B Gene

NURSA nuclear receptor signaling pathways regulating expression of PRPF40B Gene:


SOURCE GeneReport for Unigene cluster for PRPF40B Gene:


mRNA Expression by UniProt/SwissProt for PRPF40B Gene:

Tissue specificity: Expressed in the striatum and cortex of the brain (at protein level). Highly expressed in testis, fetal kidney and fetal brain. Moderately expressed in pancreas, skeletal muscle, placenta, brain and heart. Weakly expressed in colon, ileum, ovary, prostate, spleen, kidney and fetal lung.

Evidence on tissue expression from TISSUES for PRPF40B Gene

  • Skin(4.3)
  • Nervous system(4.3)
  • Intestine(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with PRPF40B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF40B Gene

Orthologs for PRPF40B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PRPF40B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PRPF40B 33 34
  • 99.55 (n)
(Canis familiaris)
Mammalia PRPF40B 33 34
  • 93.68 (n)
(Bos Taurus)
Mammalia PRPF40B 33 34
  • 93.59 (n)
(Rattus norvegicus)
Mammalia Prpf40b 33
  • 90.82 (n)
(Mus musculus)
Mammalia Prpf40b 33 16 34
  • 90.36 (n)
(Ornithorhynchus anatinus)
Mammalia PRPF40B 34
  • 49 (a)
(Anolis carolinensis)
Reptilia PRPF40B 34
  • 65 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf40b 33
  • 64.55 (n)
(Danio rerio)
Actinopterygii CR855359.1 34
  • 20 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008263 33
  • 57.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3542 33 34
  • 53.93 (n)
(Caenorhabditis elegans)
Secernentea ZK1098.1 34
  • 36 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E18239g 33
  • 47.98 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR159C 33
  • 45.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP40 33 34 36
  • 44.44 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11107 34
  • 47 (a)
Species where no ortholog for PRPF40B was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PRPF40B Gene

Gene Tree for PRPF40B (if available)
Gene Tree for PRPF40B (if available)

Paralogs for PRPF40B Gene

Paralogs for PRPF40B Gene

(2) SIMAP similar genes for PRPF40B Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PRPF40B: view

Variants for PRPF40B Gene

Sequence variations from dbSNP and Humsavar for PRPF40B Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000016086 -- 49,637,274(+) T/G intron_variant
rs1000016184 -- 49,634,595(+) C/G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000055983 -- 49,641,230(+) G/A intron_variant
rs1000086690 -- 49,641,547(+) C/T intron_variant
rs1000188901 -- 49,627,232(+) C/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PRPF40B Gene

Variant ID Type Subtype PubMed ID
nsv832406 CNV loss 17160897
nsv952177 CNV deletion 24416366

Variation tolerance for PRPF40B Gene

Residual Variation Intolerance Score: 6.17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.75; 33.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRPF40B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRPF40B Gene

Disorders for PRPF40B Gene

Additional Disease Information for PRPF40B

No disorders were found for PRPF40B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRPF40B Gene

Publications for PRPF40B Gene

  1. Huntingtin interacts with a family of WW domain proteins. (PMID: 9700202) Faber PW … MacDonald ME (Human molecular genetics 1998) 2 3 4 22 58
  2. Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo. (PMID: 25605964) Becerra S … Suñé C (RNA (New York, N.Y.) 2015) 2 3 58
  3. Huntingtin's WW domain partners in Huntington's disease post-mortem brain fulfill genetic criteria for direct involvement in Huntington's disease pathogenesis. (PMID: 10958656) Passani LA … MacDonald ME (Human molecular genetics 2000) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 58

Products for PRPF40B Gene

Sources for PRPF40B Gene

Loading form....