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    PRPF38B pre-mRNA processing factor 38B [ Homo sapiens (human) ]

    Gene ID: 55119, updated on 5-May-2024

    Summary

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    Official Symbol
    PRPF38Bprovided by HGNC
    Official Full Name
    pre-mRNA processing factor 38Bprovided by HGNC
    Primary source
    HGNC:HGNC:25512
    See related
    Ensembl:ENSG00000134186 AllianceGenome:HGNC:25512
    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
    NET1
    Summary
    Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of precatalytic spliceosome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lymph node (RPKM 13.4), bone marrow (RPKM 12.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p13.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108692310..108702928)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (108725575..108736181)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109234932..109245550)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109203434-109204023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109204024-109204612 Neighboring gene HEN methyltransferase 1 Neighboring gene uncharacterized LOC105378890 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109234711-109235271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:109235834-109236394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1429 Neighboring gene fibronectin type III domain containing 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:109288975-109289545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1137 Neighboring gene syntaxin binding protein 3 Neighboring gene N-acetylneuraminic acid phosphatase pseudogene

    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
    • 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. The localization of pre mRNA splicing factor PRPF38B is a novel prognostic biomarker that may predict survival benefit of trastuzumab in patients with breast cancer overexpressing HER2. Abdel-Fatah TMA, et al. Oncotarget, 2017 Dec 22. PMID 29348822, Free PMC Article
    2. Immunomic analysis of human sarcoma. Lee SY, et al. Proc Natl Acad Sci U S A, 2003 Mar 4. PMID 12601173, Free PMC Article
    3. Identification of UHRF1/2 as new N-methylpurine DNA glycosylase-interacting proteins. Liang C, et al. Biochem Biophys Res Commun, 2013 Apr 19. PMID 23537643
    4. Global phosphoproteome of HT-29 human colon adenocarcinoma cells. Kim JE, et al. J Proteome Res, 2005 Jul-Aug. PMID 16083285
    5. The E3 ubiquitin ligase UBR5 interacts with the H/ACA ribonucleoprotein complex and regulates ribosomal RNA biogenesis in embryonic stem cells. Saez I, et al. FEBS Lett, 2020 Jan. PMID 31365120

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of PRP38 pre-mRNA processing factor 38 (yeast) domain containing B (PRPF38B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10330, MGC41809, MGC163218

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-splicing factor 38B
    Names
    PRP38 pre-mRNA processing factor 38 domain containing B
    sarcoma antigen NY-SAR-27

    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_001349757.2 → NP_001336686.1  pre-mRNA-splicing factor 38B isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) encodes isoform b.
      Source sequence(s)
      AL591719, AL833950, DA039951
      Consensus CDS
      CCDS86003.1
      UniProtKB/TrEMBL
      A0A0A0MRN0
      Related
      ENSP00000359038.1, ENST00000370021.1
      Conserved Domains (2) summary
      TIGR01642
      Location:352 → 434
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam03371
      Location:15 → 116
      PRP38; PRP38 family

    2. NM_001349758.2 → NP_001336687.1  pre-mRNA-splicing factor 38B isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variant 9, encodes isoform e.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (2) summary
      pfam03371
      Location:7 → 43
      PRP38; PRP38 family
      cl25887
      Location:279 → 361
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

    3. NM_001349759.2 → NP_001336688.1  pre-mRNA-splicing factor 38B isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), as well as variant 8, encodes isoform e.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (2) summary
      pfam03371
      Location:7 → 43
      PRP38; PRP38 family
      cl25887
      Location:279 → 361
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

    4. NM_001349761.2 → NP_001336690.1  pre-mRNA-splicing factor 38B isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variant 4, encodes isoform c.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (2) summary
      TIGR01642
      Location:318 → 400
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam03371
      Location:1 → 82
      PRP38; PRP38 family

    5. NM_001349762.2 → NP_001336691.1  pre-mRNA-splicing factor 38B isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variant 3, encodes isoform c.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (2) summary
      TIGR01642
      Location:318 → 400
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam03371
      Location:1 → 82
      PRP38; PRP38 family

    6. NM_001349763.2 → NP_001336692.1  pre-mRNA-splicing factor 38B isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5), as well as variants 6 and 7, encodes isoform d.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:281 → 363
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    7. NM_001349764.2 → NP_001336693.1  pre-mRNA-splicing factor 38B isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6), as well as variants 5 and 7, encodes isoform d.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:281 → 363
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    8. NM_001349765.2 → NP_001336694.1  pre-mRNA-splicing factor 38B isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7), as well as variants 5 and 6, encodes isoform d.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:281 → 363
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    9. NM_001349766.2 → NP_001336695.1  pre-mRNA-splicing factor 38B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10), as well as variants 11-15, encodes isoform f.
      Source sequence(s)
      AL591719, BC144243, DA039951
      Conserved Domains (1) summary
      TIGR01642
      Location:266 → 348
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    10. NM_001349767.2 → NP_001336696.1  pre-mRNA-splicing factor 38B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11), as well as variants 10 and 12-15, encodes isoform f.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:266 → 348
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    11. NM_001349768.2 → NP_001336697.1  pre-mRNA-splicing factor 38B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12), as well as variants 10, 11, and 13-15, encodes isoform f.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:266 → 348
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    12. NM_001349769.2 → NP_001336698.1  pre-mRNA-splicing factor 38B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (13), as well as variants 10-12, 14, and 15, encodes isoform f.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:266 → 348
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    13. NM_001349770.2 → NP_001336699.1  pre-mRNA-splicing factor 38B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (14), as well as variants 10-13 and 15, encodes isoform f.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:266 → 348
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    14. NM_001349771.2 → NP_001336700.1  pre-mRNA-splicing factor 38B isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (15), as well as variants 10-14, encodes isoform f.
      Source sequence(s)
      AL160171, AL591719
      Conserved Domains (1) summary
      TIGR01642
      Location:266 → 348
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

    15. NM_018061.4 → NP_060531.2  pre-mRNA-splicing factor 38B isoform a

      See identical proteins and their annotated locations for NP_060531.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AL591719, BC130346, DA039951
      Consensus CDS
      CCDS788.1
      UniProtKB/Swiss-Prot
      Q05DD6, Q32Q58, Q5VTL8, Q5VTL9, Q6PK39, Q7Z6E2, Q86WF3, Q8IWG9, Q9NW40
      Related
      ENSP00000359042.4, ENST00000370025.9
      Conserved Domains (2) summary
      TIGR01642
      Location:463 → 545
      U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
      pfam03371
      Location:47 → 227
      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
      108692310..108702928
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541687.4 → XP_011539989.1  pre-mRNA-splicing factor 38B isoform X2

      See identical proteins and their annotated locations for XP_011539989.1

      Conserved Domains (1) summary
      pfam03371
      Location:47 → 186
      PRP38; PRP38 family

    2. XM_047423902.1 → XP_047279858.1  pre-mRNA-splicing factor 38B isoform X2

      Related
      ENSP00000359039.5, ENST00000370022.9

    3. XM_047423900.1 → XP_047279856.1  pre-mRNA-splicing factor 38B isoform X1

    RNA

    1. XR_007061357.1 RNA Sequence

    2. XR_007061358.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      108725575..108736181
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337343.1 → XP_054193318.1  pre-mRNA-splicing factor 38B isoform X2

    2. XM_054337342.1 → XP_054193317.1  pre-mRNA-splicing factor 38B isoform X2

    3. XM_054337340.1 → XP_054193315.1  pre-mRNA-splicing factor 38B isoform X1

    4. XM_054337341.1 → XP_054193316.1  pre-mRNA-splicing factor 38B isoform X3

    RNA

    1. XR_008486085.1 RNA Sequence

    2. XR_008486086.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VTL8.1 GenPept UniProtKB/Swiss-Prot:Q5VTL8

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