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

Gene ID: 55119, updated on 21-Dec-2019

Summary

Official Symbol
PRPF38Bprovided by HGNC
Official Full Name
pre-mRNA processing factor 38Bprovided by HGNC
Primary source
HGNC:HGNC:25512
See related
Ensembl:ENSG00000134186
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
Expression
Ubiquitous expression in lymph node (RPKM 13.4), bone marrow (RPKM 12.6) and 25 other tissues See more
Orthologs

Genomic context

See PRPF38B in Genome Data Viewer
Location:
1p13.3
Exon count:
8
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (108692310..108702928)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109234932..109244425)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene HEN methyltransferase 1 Neighboring gene uncharacterized LOC105378890 Neighboring gene fibronectin type III domain containing 7 Neighboring gene syntaxin binding protein 3 Neighboring gene N-acetylneuraminic acid phosphatase pseudogene

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 (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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10330, MGC41809, MGC163218

Gene Ontology Provided by GOA

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

General protein information

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)

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_001349757.2NP_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
    Related
    ENSP00000359038.1, ENST00000370021.1
    Conserved Domains (2) summary
    pfam03371
    Location:15116
    PRP38; PRP38 family
    cl25887
    Location:352434
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  2. NM_001349758.2NP_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:743
    PRP38; PRP38 family
    cl25887
    Location:279361
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  3. NM_001349759.2NP_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:743
    PRP38; PRP38 family
    cl25887
    Location:279361
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  4. NM_001349761.2NP_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
    pfam03371
    Location:182
    PRP38; PRP38 family
    cl25887
    Location:318400
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  5. NM_001349762.2NP_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
    pfam03371
    Location:182
    PRP38; PRP38 family
    cl25887
    Location:318400
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  6. NM_001349763.2NP_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 (2) summary
    pfam03371
    Location:445
    PRP38; PRP38 family
    cl25887
    Location:281363
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  7. NM_001349764.2NP_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 (2) summary
    pfam03371
    Location:445
    PRP38; PRP38 family
    cl25887
    Location:281363
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  8. NM_001349765.2NP_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 (2) summary
    pfam03371
    Location:445
    PRP38; PRP38 family
    cl25887
    Location:281363
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  9. NM_001349766.2NP_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 (2) summary
    pfam03371
    Location:130
    PRP38; PRP38 family
    cl25887
    Location:266348
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  10. NM_001349767.2NP_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 (2) summary
    pfam03371
    Location:130
    PRP38; PRP38 family
    cl25887
    Location:266348
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  11. NM_001349768.2NP_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 (2) summary
    pfam03371
    Location:130
    PRP38; PRP38 family
    cl25887
    Location:266348
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  12. NM_001349769.2NP_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 (2) summary
    pfam03371
    Location:130
    PRP38; PRP38 family
    cl25887
    Location:266348
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  13. NM_001349770.2NP_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 (2) summary
    pfam03371
    Location:130
    PRP38; PRP38 family
    cl25887
    Location:266348
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  14. NM_001349771.2NP_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 (2) summary
    pfam03371
    Location:130
    PRP38; PRP38 family
    cl25887
    Location:266348
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
  15. NM_018061.4NP_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
    Q5VTL8
    Related
    ENSP00000359042.4, ENST00000370025.9
    Conserved Domains (2) summary
    pfam03371
    Location:47227
    PRP38; PRP38 family
    cl25887
    Location:463545
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    108692310..108702928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541687.3XP_011539989.1  pre-mRNA-splicing factor 38B isoform X2

    See identical proteins and their annotated locations for XP_011539989.1

    Related
    ENSP00000359039.5, ENST00000370022.9
    Conserved Domains (1) summary
    pfam03371
    Location:47186
    PRP38; PRP38 family
  2. XM_017001597.1XP_016857086.1  pre-mRNA-splicing factor 38B isoform X1

    Conserved Domains (2) summary
    pfam03371
    Location:743
    PRP38; PRP38 family
    cl25887
    Location:279361
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

RNA

  1. XR_001737263.2 RNA Sequence

  2. XR_001737264.2 RNA Sequence

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