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PRPF38A pre-mRNA processing factor 38A [ Homo sapiens (human) ]

Gene ID: 84950, updated on 27-Aug-2024

Summary

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Official Symbol
PRPF38Aprovided by HGNC
Official Full Name
pre-mRNA processing factor 38Aprovided by HGNC
Primary source
HGNC:HGNC:25930
See related
Ensembl:ENSG00000134748 MIM:617031; AllianceGenome:HGNC:25930
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Prp38; PRP38A
Summary
Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 12.2), ovary (RPKM 11.7) and 25 other tissues See more
Orthologs
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Genomic context

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See PRPF38A in Genome Data Viewer
Location:
1p32.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (52404602..52420836)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52286071..52302304)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (52870274..52886508)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr1:52815874-52816848 and GRCh37_chr1:52816849-52817822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:52822843-52823344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 889 Neighboring gene coiled-coil and C2 domain containing 1B Neighboring gene phospholipase A2 group XIIA pseudogene 1 Neighboring gene origin recognition complex subunit 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:52869594-52870793 Neighboring gene uncharacterized LOC124904850 Neighboring gene Sharpr-MPRA regulatory region 15542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1032 Neighboring gene terminal uridylyl transferase 4 Neighboring gene MPRA-validated peak227 silencer Neighboring gene MPRA-validated peak228 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:52963547-52964066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:52964067-52964586 Neighboring gene uncharacterized LOC105378723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 890 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53036969-53037469 Neighboring gene eukaryotic translation elongation factor 1 gamma pseudogene 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Townsend C, et al. Science, 2020 Dec 18. PMID 33243851
  2. Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins. Dopie J, et al. J Cell Biol, 2020 Sep 7. PMID 32609799, Free PMC Article
  3. Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival. Chan S, et al. Mol Cancer Ther, 2017 Dec. PMID 28878028, Free PMC Article
  4. Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome. Schütze T, et al. RNA, 2016 Feb. PMID 26673105, Free PMC Article
  5. Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor. Ulrich AK, et al. BMC Evol Biol, 2017 Mar 24. PMID 28335716, Free PMC Article

See all (73) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
    Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
  2. Multiple protein-protein interactions are converging on the Prp38 protein during activation of the human spliceosome.
    Title: Multiple protein-protein interactions converging on the Prp38 protein during activation of the human spliceosome.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of PRP38 pre-mRNA processing factor 38 domain containing A (PRPF38A) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC3320, FLJ14936

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
pre-mRNA-splicing factor 38A
Names
PRP38 pre-mRNA processing factor 38 domain containing A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_032864.4 → NP_116253.2  pre-mRNA-splicing factor 38A

    See identical proteins and their annotated locations for NP_116253.2

    Status: VALIDATED

    Source sequence(s)
    AK092038, AL138849, BE465896, BF223635, BU508261
    Consensus CDS
    CCDS567.1
    UniProtKB/Swiss-Prot
    Q8NAV1, Q96JW1, Q9BVZ8
    Related
    ENSP00000257181.8, ENST00000257181.10
    Conserved Domains (1) summary
    pfam03371
    Location:10 → 172
    PRP38; PRP38 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    52404602..52420836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    52286071..52302304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032284.2: Suppressed sequence

    Description
    NM_032284.2: This RefSeq was permanently suppressed because it contains the wrong CDS.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NAV1.1 GenPept UniProtKB/Swiss-Prot:Q8NAV1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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