Aliases for PRPF38B Gene

Aliases for PRPF38B Gene

  • Pre-MRNA Processing Factor 38B 2 3 5
  • Pre-MRNA-Splicing Factor 38B 3 4
  • Sarcoma Antigen NY-SAR-27 3 4
  • PRP38 Pre-MRNA Processing Factor 38 (Yeast) Domain Containing B 2
  • PRP38 Pre-MRNA Processing Factor 38 Domain Containing B 3
  • NET1 3

External Ids for PRPF38B Gene

Previous GeneCards Identifiers for PRPF38B Gene

  • GC01P108948
  • GC01P109036
  • GC01P109234
  • GC01P107127

Summaries for PRPF38B Gene

GeneCards Summary for PRPF38B Gene

PRPF38B (Pre-MRNA Processing Factor 38B) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway.

UniProtKB/Swiss-Prot Summary for PRPF38B Gene

Additional gene information for PRPF38B Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRPF38B Gene

Genomics for PRPF38B Gene

GeneHancer (GH) Regulatory Elements for PRPF38B Gene

Promoters and enhancers for PRPF38B 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
GH01J108691 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 761.1 +1.3 1326 6 ZBTB40 CTCF GATA3 ZBTB6 LCORL RBPJ POLR2A TCF7L2 NR2F6 ATF1 PRPF38B lnc-HENMT1-2 ENSG00000232971 ENSG00000228703 NONHSAG002311.2
GH01J109482 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 86.1 +791.8 791822 2.6 ZNF785 SP1 ZBTB40 SIX5 ZBTB6 RBPJ SMARCE1 POLR2A CTBP1 HCFC1 ATXN7L2 ENSG00000258634 STRIP1 PRPF38B ENSG00000244716 ENSG00000273373 SYPL2 ENSG00000228665 CLCC1 RBM15
GH01J109099 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas dbSUPER 61.6 +408.4 408409 2.6 ZNF785 SIN3A SP1 ZBTB40 CTCF ZBTB6 LCORL FOXA1 MLX RBPJ ENSG00000270066 SCARNA2 ENSG00000258634 PRPF38B STRIP1 C1orf194 ENSG00000244716 ENSG00000228665 GPR61 ENSG00000232971
GH01J108197 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 47.3 -492.6 -492636 3.9 E2F8 ZNF785 ZBTB40 CTCF SREBF1 SMARCE1 POLR2A ZNF217 ZNF133 CC2D1A SLC25A24 ENSG00000260879 ENSG00000280186 PRPF38B ENSG00000244716 ENSG00000228665 ENSG00000226822 FAM102B piR-36393-028
GH01J109088 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 43.4 +398.8 398789 4.6 GTF3C2 FOXK2 SIN3A ZNF24 ZBTB40 SP1 CTCF SREBF1 SIX5 ZBTB6 TMEM167B ENSG00000273382 LOC105378892 NDUFB3P1 NONHSAG002324.2 ENSG00000258634 PRPF38B STRIP1 C1orf194 ENSG00000228665
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRPF38B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRPF38B gene promoter:
  • AREB6
  • Bach2
  • CUTL1
  • GATA-6
  • HNF-1
  • HNF-1A
  • Nkx2-5
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)

Genomic Locations for PRPF38B Gene

Genomic Locations for PRPF38B Gene
chr1:108,692,292-108,702,928
(GRCh38/hg38)
Size:
10,637 bases
Orientation:
Plus strand
chr1:109,234,932-109,244,425
(GRCh37/hg19)
Size:
9,494 bases
Orientation:
Plus strand

Genomic View for PRPF38B Gene

Genes around PRPF38B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF38B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRPF38B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF38B Gene

Proteins for PRPF38B Gene

  • Protein details for PRPF38B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VTL8-PR38B_HUMAN
    Recommended name:
    Pre-mRNA-splicing factor 38B
    Protein Accession:
    Q5VTL8
    Secondary Accessions:
    • Q05DD6
    • Q32Q58
    • Q5VTL9
    • Q6PK39
    • Q7Z6E2
    • Q86WF3
    • Q8IWG9
    • Q9NW40

    Protein attributes for PRPF38B Gene

    Size:
    546 amino acids
    Molecular mass:
    64468 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAO65168.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PRPF38B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRPF38B Gene

Post-translational modifications for PRPF38B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRPF38B Gene

Domains & Families for PRPF38B Gene

Gene Families for PRPF38B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PRPF38B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRPF38B Gene

GenScript: Design optimal peptide antigens:
  • Sarcoma antigen NY-SAR-27 (PR38B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5VTL8

UniProtKB/Swiss-Prot:

PR38B_HUMAN :
  • Belongs to the PRP38 family.
Family:
  • Belongs to the PRP38 family.
genes like me logo Genes that share domains with PRPF38B: view

Function for PRPF38B Gene

Molecular function for PRPF38B Gene

UniProtKB/Swiss-Prot Function:
May be required for pre-mRNA splicing.

Phenotypes From GWAS Catalog for PRPF38B Gene

Gene Ontology (GO) - Molecular Function for PRPF38B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
genes like me logo Genes that share ontologies with PRPF38B: view
genes like me logo Genes that share phenotypes with PRPF38B: view

Animal Models for PRPF38B Gene

MGI Knock Outs for PRPF38B:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRPF38B Gene

Localization for PRPF38B Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF38B 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 PRPF38B gene
Compartment Confidence
nucleus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for PRPF38B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005681 spliceosomal complex IEA --
GO:0071011 precatalytic spliceosome IBA 21873635
genes like me logo Genes that share ontologies with PRPF38B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PRPF38B Gene

Pathways & Interactions for PRPF38B Gene

PathCards logo

SuperPathways for PRPF38B Gene

SuperPathway Contained pathways
1 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with PRPF38B: view

Pathways by source for PRPF38B Gene

1 KEGG pathway for PRPF38B Gene

Gene Ontology (GO) - Biological Process for PRPF38B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with PRPF38B: view

No data available for SIGNOR curated interactions for PRPF38B Gene

Drugs & Compounds for PRPF38B Gene

No Compound Related Data Available

Transcripts for PRPF38B Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF38B Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b
SP1: - -
SP2: - - - - - - -
SP3: - - - - -
SP4: - - - -
SP5: - -
SP6:
SP7: -
SP8:

Relevant External Links for PRPF38B Gene

GeneLoc Exon Structure for
PRPF38B
ECgene alternative splicing isoforms for
PRPF38B

Expression for PRPF38B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRPF38B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRPF38B Gene

This gene is overexpressed in Lymph node (13.2), Peripheral blood mononuclear cells (10.2), and NK cells (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRPF38B Gene



Protein tissue co-expression partners for PRPF38B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF38B Gene:

PRPF38B

SOURCE GeneReport for Unigene cluster for PRPF38B Gene:

Hs.342307

Evidence on tissue expression from TISSUES for PRPF38B Gene

  • Lung(4.4)
  • Muscle(4.3)
  • Skin(4.3)
  • Nervous system(2.3)
  • Liver(2.1)
  • Spleen(2.1)
  • Intestine(2)
genes like me logo Genes that share expression patterns with PRPF38B: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF38B Gene

Orthologs for PRPF38B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF38B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRPF38B 33 32
  • 99.94 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PRPF38B 33 32
  • 94.14 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRPF38B 33
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PRPF38B 33 32
  • 92.76 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRPF38B 33
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Prpf38b 32
  • 88.75 (n)
mouse
(Mus musculus)
Mammalia Prpf38b 17 33 32
  • 86.08 (n)
chicken
(Gallus gallus)
Aves PRPF38B 33 32
  • 80.95 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRPF38B 33
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf38b 32
  • 78.01 (n)
Str.11052 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.8346 32
zebrafish
(Danio rerio)
Actinopterygii prpf38b 33 32
  • 73.91 (n)
OneToOne
wufc43b05 32
fruit fly
(Drosophila melanogaster)
Insecta CG1622 33
  • 48 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y108G3AL.2 33
  • 39 (a)
OneToOne
rice
(Oryza sativa)
Liliopsida Os.10119 32
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10416 33
  • 57 (a)
OneToOne
Cin.9541 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9541 32
Species where no ortholog for PRPF38B 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)
  • 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 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 PRPF38B Gene

ENSEMBL:
Gene Tree for PRPF38B (if available)
TreeFam:
Gene Tree for PRPF38B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRPF38B: view image

Paralogs for PRPF38B Gene

No data available for Paralogs for PRPF38B Gene

Variants for PRPF38B Gene

Sequence variations from dbSNP and Humsavar for PRPF38B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs761679182 uncertain-significance, Severe Myopia 108,699,701(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs386352353 uncertain-significance, not provided 108,699,842(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1000130284 -- 108,691,792(+) T/C upstream_transcript_variant
rs1000397344 -- 108,691,508(+) CTCTCTCTCTCTC/CTCTCTCTC/CTCTCTCTCTC/CTCTCTCTCTCTCTC upstream_transcript_variant
rs1000406187 -- 108,692,224(+) G/A upstream_transcript_variant

Variation tolerance for PRPF38B Gene

Residual Variation Intolerance Score: 25.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.20; 39.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRPF38B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRPF38B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for PRPF38B Gene

Disorders for PRPF38B Gene

Additional Disease Information for PRPF38B

No disorders were found for PRPF38B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRPF38B Gene

Publications for PRPF38B Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  2. Immunomic analysis of human sarcoma. (PMID: 12601173) Lee SY … Scanlan MJ (Proceedings of the National Academy of Sciences of the United States of America 2003) 3 4 56
  3. Insights into the ubiquitin-proteasome system of human embryonic stem cells. (PMID: 29511261) Saez I … Vilchez D (Scientific reports 2018) 3 56
  4. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3 56
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56

Products for PRPF38B Gene

Sources for PRPF38B Gene