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Aliases for PRPF38A Gene

Aliases for PRPF38A Gene

  • Pre-MRNA Processing Factor 38A 2 3 5
  • PRP38 Pre-MRNA Processing Factor 38 (Yeast) Domain Containing A 2
  • PRP38 Pre-MRNA Processing Factor 38 Domain Containing A 3
  • Pre-MRNA-Splicing Factor 38A 3
  • PRP38A 3
  • Prp38 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. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway.

UniProtKB/Swiss-Prot for PRPF38A Gene

  • May be required for pre-mRNA splicing.

Additional gene information for PRPF38A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF38A Gene

Genomics for PRPF38A Gene

GeneHancer (GH) Regulatory Elements for PRPF38A Gene

Promoters and enhancers for PRPF38A 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
GH01I052402 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 561.3 -0.3 -265 3.2 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 PRPF38A ORC1 MAGOH KTI12 ENSG00000266993 TXNDC12 PLA2G12AP1
GH01I051874 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 23.1 -527.1 -527080 5.3 CLOCK MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 NFYC NRDC ENSG00000266993 ZCCHC11 PRPF38A CC2D1B ZFYVE9 LINC01562 TXNDC12 RPS13P2 KTI12
GH01I052364 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 28.2 -38.9 -38881 3.2 HDGF PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 YY1 CC2D1B PRPF38A ZCCHC11 MAGOH ENSG00000230953 ENSG00000266993 ORC1 LOC100190934 RPS13P2 GPX7
GH01I052138 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 24 -263.3 -263343 4.8 HDGF SMAD1 FOXA2 ARNT ZFP64 ARID4B SIN3A ZNF2 ZNF766 ZNF207 ZFYVE9 PRPF38A ZCCHC11 RPS13P2 ENSG00000230953 ENSG00000266993 PODN CC2D1B LOC100190934 GPX7
GH01I052725 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 19.4 +322.4 322354 2.2 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 ZNF2 E2F8 SP3 ZNF592 ZYG11B PRPF38A ORC1 MAGOH RPS13P2 ECHDC2 ENSG00000230953 ENSG00000266993 ZYG11A GC01P052729
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRPF38A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRPF38A gene promoter:

Genomic Locations for PRPF38A Gene

Genomic Locations for PRPF38A Gene
chr1:52,404,547-52,420,839
(GRCh38/hg38)
Size:
16,293 bases
Orientation:
Plus strand
chr1:52,870,219-52,886,511
(GRCh37/hg19)

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:
    Q8NAV1-PR38A_HUMAN
    Recommended name:
    Pre-mRNA-splicing factor 38A
    Protein Accession:
    Q8NAV1
    Secondary Accessions:
    • Q96JW1
    • Q9BVZ8

    Protein attributes for PRPF38A Gene

    Size:
    312 amino acids
    Molecular mass:
    37477 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for PRPF38A Gene

Post-translational modifications for PRPF38A Gene

  • Ubiquitination at Lys23 and isoforms=118

Other Protein References for PRPF38A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRPF38A Gene

Domains & Families for PRPF38A Gene

Gene Families for PRPF38A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PRPF38A Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRPF38A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NAV1

UniProtKB/Swiss-Prot:

PR38A_HUMAN :
  • Belongs to the PRP38 family.
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:
May be required for pre-mRNA splicing.

Gene Ontology (GO) - Molecular Function for PRPF38A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA,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

Animal Model Products

CRISPR Products

miRNA for PRPF38A Gene

miRTarBase miRNAs that target PRPF38A

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

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 PRPF38A gene
Compartment Confidence
nucleus 5
cytosol 1

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 IDA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0031965 nuclear membrane IDA --
GO:0071011 precatalytic spliceosome IBA --
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

Unigene Clusters for PRPF38A Gene

PRP38 pre-mRNA processing factor 38 (yeast) domain containing A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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: - - - - -
SP3:
SP4: -

Relevant External Links for PRPF38A Gene

GeneLoc Exon Structure for
PRPF38A
ECgene alternative splicing isoforms for
PRPF38A

Expression for PRPF38A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for PRPF38A Gene



Protein tissue co-expression partners for PRPF38A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF38A Gene:

PRPF38A

SOURCE GeneReport for Unigene cluster for PRPF38A Gene:

Hs.5301

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

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
chimpanzee
(Pan troglodytes)
Mammalia PRPF38A 33 34
  • 99.68 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 98 (a)
OneToMany
-- 34
  • 84 (a)
OneToMany
dog
(Canis familiaris)
Mammalia PRPF38A 33 34
  • 93.38 (n)
cow
(Bos Taurus)
Mammalia PRPF38A 33 34
  • 92.84 (n)
rat
(Rattus norvegicus)
Mammalia Prpf38a 33
  • 89.32 (n)
mouse
(Mus musculus)
Mammalia Prpf38a 33 16 34
  • 88.46 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PRPF38A 34
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRPF38A 33 34
  • 79.59 (n)
lizard
(Anolis carolinensis)
Reptilia PRPF38A 34
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf38a 33
  • 74.06 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1823 33
zebrafish
(Danio rerio)
Actinopterygii prpf38a 33 34
  • 70.51 (n)
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3597 33
fruit fly
(Drosophila melanogaster)
Insecta Prp38 34
  • 54 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea prp-38 34
  • 49 (a)
OneToOne
barley
(Hordeum vulgare)
Liliopsida Hv.10890 33
rice
(Oryza sativa)
Liliopsida Os.6813 33
wheat
(Triticum aestivum)
Liliopsida Ta.25546 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6867 34
  • 65 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU00662 33
  • 54.97 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp38 33
  • 52.61 (n)
Species where no ortholog for PRPF38A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

ENSEMBL:
Gene Tree for PRPF38A (if available)
TreeFam:
Gene Tree for PRPF38A (if available)

Paralogs for PRPF38A Gene

Pseudogenes.org 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

Sequence variations from dbSNP and Humsavar for PRPF38A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs886046401 uncertain-significance, Meier-Gorlin syndrome 52,404,439(+) G/C upstream_transcript_variant
rs1000138712 -- 52,410,033(+) G/A intron_variant
rs1000280713 -- 52,419,811(+) G/A downstream_transcript_variant
rs1000356802 -- 52,413,496(+) A/G intron_variant
rs1000389479 -- 52,414,244(+) C/T intron_variant

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
PRPF38A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for PRPF38A Gene

Disorders for PRPF38A Gene

Additional Disease Information for PRPF38A

No disorders were found for PRPF38A Gene.

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

Publications for PRPF38A Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. 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 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor. (PMID: 28335716) Ulrich AK … Wahl MC (BMC evolutionary biology 2017) 3 58
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 58

Products for PRPF38A Gene

Sources for PRPF38A Gene

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