Aliases for PRPF38A Gene

Aliases for PRPF38A Gene

  • Pre-MRNA Processing Factor 38A 2 3 5
  • Pre-MRNA-Splicing Factor 38A 3 4
  • Prp38 2 3
  • PRP38 Pre-MRNA Processing Factor 38 (Yeast) Domain Containing A 2
  • PRP38 Pre-MRNA Processing Factor 38 Domain Containing A 3
  • FLJ14936 2
  • PRPF38A 5
  • PRP38A 3

External Ids for PRPF38A Gene

Previous GeneCards Identifiers for PRPF38A Gene

  • GC01P052583
  • GC01P052642
  • GC01P052870
  • GC01P050986

Summaries for PRPF38A Gene

GeneCards Summary for PRPF38A Gene

PRPF38A (Pre-MRNA Processing Factor 38A) is a Protein Coding gene. Diseases associated with PRPF38A include Autosomal Dominant Wolfram Syndrome and Cloacal Exstrophy. Among its related pathways are mRNA Splicing - Major Pathway and MECP2 and Associated Rett Syndrome.

UniProtKB/Swiss-Prot Summary for PRPF38A Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRPF38A Gene

Genomics for PRPF38A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PRPF38A 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 PRPF38A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRPF38A

Top Transcription factor binding sites by QIAGEN in the PRPF38A gene promoter:
  • ATF6
  • Gfi-1
  • Meis-1
  • Meis-1a
  • Meis-1b
  • Pbx1a
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • STAT5A

Genomic Locations for PRPF38A Gene

Latest Assembly
16,273 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
16,235 bases
Plus strand

(GRCh37/hg19 by Ensembl)
16,276 bases
Plus strand

Genomic View for PRPF38A Gene

Genes around PRPF38A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF38A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRPF38A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF38A Gene

Proteins for PRPF38A Gene

  • Protein details for PRPF38A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pre-mRNA-splicing factor 38A
    Protein Accession:
    Secondary Accessions:
    • Q96JW1
    • Q9BVZ8

    Protein attributes for PRPF38A Gene

    312 amino acids
    Molecular mass:
    37477 Da
    Quaternary structure:
    • Component of the spliceosome B complex (Probable) (PubMed:28781166). Interacts (via N-terminal interaction domain) with ZMAT2 AND MFAP1 (Probable) (PubMed:27773687).
    • Sequence=BAB55405.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRPF38A Gene

    Alternative splice isoforms for PRPF38A Gene


neXtProt entry for PRPF38A Gene

Post-translational modifications for PRPF38A Gene

  • Ubiquitination at Lys23 and Lys118
  • Modification sites at PhosphoSitePlus

Other Protein References for PRPF38A Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Santa Cruz Biotechnology (SCBT) Antibodies for PRPF38A

No data available for DME Specific Peptides for PRPF38A Gene

Domains & Families for PRPF38A Gene

Gene Families for PRPF38A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PRPF38A Gene


Suggested Antigen Peptide Sequences for PRPF38A Gene

GenScript: Design optimal peptide antigens:
  • Pre-mRNA-splicing factor 38A (PR38A_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PRP38 family.
  • Belongs to the PRP38 family.
genes like me logo Genes that share domains with PRPF38A: view

Function for PRPF38A Gene

Molecular function for PRPF38A Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as a component of the spliceosome.

Phenotypes From GWAS Catalog for PRPF38A Gene

Gene Ontology (GO) - Molecular Function for PRPF38A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0005515 protein binding IPI 22365833
genes like me logo Genes that share ontologies with PRPF38A: view
genes like me logo Genes that share phenotypes with PRPF38A: view

miRNA for PRPF38A Gene

miRTarBase miRNAs that target PRPF38A

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF38A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRPF38A Gene

Localization for PRPF38A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF38A 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 PRPF38A gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRPF38A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 28781166
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0071005 U2-type precatalytic spliceosome IDA 28781166
GO:0071011 precatalytic spliceosome IBA,IDA 26673105
genes like me logo Genes that share ontologies with PRPF38A: view

Pathways & Interactions for PRPF38A Gene

genes like me logo Genes that share pathways with PRPF38A: view

Pathways by source for PRPF38A Gene

1 KEGG pathway for PRPF38A Gene

Gene Ontology (GO) - Biological Process for PRPF38A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with PRPF38A: view

No data available for SIGNOR curated interactions for PRPF38A Gene

Drugs & Compounds for PRPF38A Gene

No Compound Related Data Available

Transcripts for PRPF38A Gene

mRNA/cDNA for PRPF38A Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF38A

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF38A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b
SP1: - -
SP2: - - - - -
SP4: -

Relevant External Links for PRPF38A Gene

GeneLoc Exon Structure for

Expression for PRPF38A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRPF38A Gene

Protein differential expression in normal tissues from HIPED for PRPF38A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.9), Heart (6.9), and CD8 Tcells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRPF38A Gene

Protein tissue co-expression partners for PRPF38A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRPF38A

SOURCE GeneReport for Unigene cluster for PRPF38A Gene:


Evidence on tissue expression from TISSUES for PRPF38A Gene

  • Nervous system(4.8)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with PRPF38A: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF38A Gene

Orthologs for PRPF38A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF38A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PRPF38A 29 30
  • 99.68 (n)
(Monodelphis domestica)
Mammalia -- 30
  • 98 (a)
-- 30
  • 84 (a)
(Canis familiaris)
Mammalia PRPF38A 29 30
  • 93.38 (n)
(Bos Taurus)
Mammalia PRPF38A 29 30
  • 92.84 (n)
(Rattus norvegicus)
Mammalia Prpf38a 29
  • 89.32 (n)
(Mus musculus)
Mammalia Prpf38a 29 16 30
  • 88.46 (n)
(Ornithorhynchus anatinus)
Mammalia PRPF38A 30
  • 64 (a)
(Gallus gallus)
Aves PRPF38A 29 30
  • 79.59 (n)
(Anolis carolinensis)
Reptilia PRPF38A 30
  • 96 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia prpf38a 29
  • 74.06 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1823 29
(Danio rerio)
Actinopterygii prpf38a 29 30
  • 70.51 (n)
-- 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3597 29
Fruit Fly
(Drosophila melanogaster)
Insecta Prp38 30
  • 54 (a)
(Caenorhabditis elegans)
Secernentea prp-38 30
  • 49 (a)
(Hordeum vulgare)
Liliopsida Hv.10890 29
(Oryza sativa)
Liliopsida Os.6813 29
(Triticum aestivum)
Liliopsida Ta.25546 29
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6867 30
  • 65 (a)
Bread mold
(Neurospora crassa)
Ascomycetes NCU00662 29
  • 54.97 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp38 29
  • 52.61 (n)
Species where no ortholog for PRPF38A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • 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)
  • 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)

Evolution for PRPF38A Gene

Gene Tree for PRPF38A (if available)
Gene Tree for PRPF38A (if available)
Evolutionary constrained regions (ECRs) for PRPF38A: view image
Alliance of Genome Resources:
Additional Orthologs for PRPF38A

Paralogs for PRPF38A Gene Pseudogenes for PRPF38A Gene

genes like me logo Genes that share paralogs with PRPF38A: view

No data available for Paralogs for PRPF38A Gene

Variants for PRPF38A Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PRPF38A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Variation tolerance for PRPF38A Gene

Residual Variation Intolerance Score: 25.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.29; 6.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRPF38A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Structural Variations from Database of Genomic Variants (DGV) for PRPF38A Gene

Disorders for PRPF38A Gene

MalaCards: The human disease database

(4) MalaCards diseases for PRPF38A Gene - From: COP

Disorder Aliases PubMed IDs
autosomal dominant wolfram syndrome
cloacal exstrophy
  • omphalocele, exstrophy of the cloaca, imperforate anus, and spinal defects complex
bladder exstrophy-epispadias-cloacal exstrophy complex
  • exstrophy-epispadias complex
retinitis pigmentosa
  • rp
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PRPF38A

genes like me logo Genes that share disorders with PRPF38A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRPF38A Gene

Publications for PRPF38A Gene

  1. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  2. Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome. (PMID: 26673105) Schütze T … Wahl MC (RNA (New York, N.Y.) 2016) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for PRPF38A Gene

Sources for PRPF38A Gene