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

Gene ID: 55119, updated on 5-Mar-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
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Genomic context

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See PRPF38B in Genome Data Viewer
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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