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] See more...

Aliases for PRPF40B Gene

Aliases for PRPF40B Gene

  • Pre-MRNA Processing Factor 40 Homolog B 2 3 5
  • HYPC 2 3 4
  • Pre-MRNA-Processing Factor 40 Homolog B 3 4
  • Huntingtin Interacting Protein C 2 3
  • Huntingtin Yeast Partner C 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
  • Huntingtin-Interacting Protein C 4
  • PRPF40B 5

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. Diseases associated with PRPF40B include Blackwater Fever and Hypoparathyroidism, X-Linked. Among its related pathways are mRNA Splicing - Major Pathway. An important paralog of this gene is PRPF40A.

UniProtKB/Swiss-Prot Summary for PRPF40B Gene

Additional gene information for PRPF40B Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRPF40B Gene

Genomics for PRPF40B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PRPF40B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRPF40B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRPF40B

Top Transcription factor binding sites by QIAGEN in the PRPF40B gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • Egr-1
  • POU2F1

Genomic Locations for PRPF40B Gene

Genomic Locations for PRPF40B Gene
chr12:49,568,218-49,645,129
(GRCh38/hg38)
Size:
76,912 bases
Orientation:
Plus strand
chr12:49,962,001-50,038,449
(GRCh37/hg19)
Size:
76,449 bases
Orientation:
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:
    Q6NWY9-PR40B_HUMAN
    Recommended name:
    Pre-mRNA-processing factor 40 homolog B
    Protein Accession:
    Q6NWY9
    Secondary Accessions:
    • O75401
    • Q6PI09
    • Q6ZWB3
    • Q8NCZ1
    • Q9H5G4
    • Q9NT95

    Protein attributes for PRPF40B Gene

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

    Alternative splice isoforms for PRPF40B Gene

    UniProtKB/Swiss-Prot:

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:
  • Huntingtin-interacting protein C (PR40B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6NWY9

UniProtKB/Swiss-Prot:

PR40B_HUMAN :
  • Belongs to the PRPF40 family.
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 21873635
GO:0005515 protein binding IEA --
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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF40B

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

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 PRPF40B gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

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 21873635
GO:0016607 nuclear speck IEA --
GO:0071004 U2-type prespliceosome IBA 21873635
genes like me logo Genes that share ontologies with PRPF40B: view

Pathways & Interactions for PRPF40B Gene

PathCards logo

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 21873635
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0045292 mRNA cis splicing, via spliceosome 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

mRNA/cDNA for PRPF40B Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF40B

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 ^
SP1:
SP2: -
SP3:
SP4:
SP5:
SP6: -
SP7: -
SP8:

ExUns: 18 ^ 19 ^ 20a · 20b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for PRPF40B Gene

GeneLoc Exon Structure for
PRPF40B

Expression for PRPF40B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for PRPF40B Gene



Protein tissue co-expression partners for PRPF40B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRPF40B

SOURCE GeneReport for Unigene cluster for PRPF40B Gene:

Hs.706827

mRNA Expression by UniProt/SwissProt for PRPF40B Gene:

Q6NWY9-PR40B_HUMAN
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

  • Nervous system(4.4)
  • Skin(4.4)
  • 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
Chimpanzee
(Pan troglodytes)
Mammalia PRPF40B 30 31
  • 99.55 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PRPF40B 30 31
  • 93.68 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PRPF40B 30 31
  • 93.59 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Prpf40b 30
  • 90.82 (n)
Mouse
(Mus musculus)
Mammalia Prpf40b 30 17 31
  • 90.36 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PRPF40B 31
  • 49 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PRPF40B 31
  • 65 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia prpf40b 30
  • 64.55 (n)
Zebrafish
(Danio rerio)
Actinopterygii CR855359.1 31
  • 20 (a)
ManyToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008263 30
  • 57.47 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG3542 30 31
  • 53.93 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ZK1098.1 31
  • 36 (a)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E18239g 30
  • 47.98 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ADR159C 30
  • 45.62 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP40 30 31 33
  • 44.44 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.11107 31
  • 47 (a)
OneToMany
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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for PRPF40B (if available)
TreeFam:
Gene Tree for PRPF40B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRPF40B: view image

Paralogs for PRPF40B Gene

Paralogs for PRPF40B Gene

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

  • PR40B_HUMAN
  • F8VU11_HUMAN
  • H0YII7_HUMAN
genes like me logo Genes that share paralogs with PRPF40B: view

Variants for PRPF40B Gene

Additional dbSNP identifiers (rs#s) for PRPF40B Gene

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
PRPF40B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRPF40B Gene

Disorders for PRPF40B Gene

MalaCards: The human disease database

(4) MalaCards diseases for PRPF40B Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
blackwater fever
  • black water fever
hypoparathyroidism, x-linked
  • hypx
rett syndrome
  • rtt
familial atrial fibrillation
  • atrial fibrillation, familial, 1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PRPF40B

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

No data available for 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 23
  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
  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
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature. (PMID: 31088860) Lorenzini PA … Roca X (RNA (New York, N.Y.) 2019) 3

Products for PRPF40B Gene

Sources for PRPF40B Gene