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

    Gene ID: 84950, updated on 5-Mar-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See PRPF38A in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (52404602..52420836)
    RS_2023_10 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

    Expression

    • Project title: 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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_032864.4NP_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:10172
      PRP38; PRP38 family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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.