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Prpf38b PRP38 pre-mRNA processing factor 38 (yeast) domain containing B [ Mus musculus (house mouse) ]

Gene ID: 66921, updated on 5-Mar-2024

Summary

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Official Symbol
Prpf38bprovided by MGI
Official Full Name
PRP38 pre-mRNA processing factor 38 (yeast) domain containing Bprovided by MGI
Primary source
MGI:MGI:1914171
See related
Ensembl:ENSMUSG00000027881 AllianceGenome:MGI:1914171
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
1110021E09Rik
Summary
Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of precatalytic spliceosome. Is expressed in several structures, including central nervous system; gut; male reproductive gland or organ; thymus; and urinary system. Orthologous to human PRPF38B (pre-mRNA processing factor 38B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 27.0), thymus adult (RPKM 25.1) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
3 F3; 3 47.92 cM
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (108810121..108819055, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (108902805..108911729, complement)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene syntaxin binding protein 3 Neighboring gene STARR-positive B cell enhancer mm9_chr3:108642483-108642783 Neighboring gene STARR-positive B cell enhancer mm9_chr3:108643371-108643672 Neighboring gene fibronectin type III domain containing 7 Neighboring gene STARR-positive B cell enhancer ABC_E3460 Neighboring gene STARR-positive B cell enhancer ABC_E4576 Neighboring gene HEN1 methyltransferase homolog 1 (Arabidopsis) Neighboring gene EEIG family member 2 Neighboring gene predicted gene 43221

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Conserved expression of ultra-conserved noncoding RNA in mammalian nervous system. Zhou J, et al. Biochim Biophys Acta Gene Regul Mech, 2017 Dec. PMID 29055695
  2. Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Murtaza N, et al. Cell Rep, 2022 Nov 22. PMID 36417873
  3. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Koscielny G, et al. Nucleic Acids Res, 2014 Jan. PMID 24194600, Free PMC Article
  4. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, et al. Development, 2000 Apr. PMID 10725249
  5. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2) 
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
pre-mRNA-splicing factor 38B

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_001356292.1 → NP_001343221.1  pre-mRNA-splicing factor 38B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL671894
    Conserved Domains (1) summary
    TIGR01642
    Location:213 → 321
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

  2. NM_025845.3 → NP_080121.1  pre-mRNA-splicing factor 38B isoform 1

    See identical proteins and their annotated locations for NP_080121.1

    Status: VALIDATED

    Source sequence(s)
    AL671894
    Consensus CDS
    CCDS17770.1
    UniProtKB/Swiss-Prot
    Q80SY5, Q9CTD9, Q9CU48, Q9CUI6
    Related
    ENSMUSP00000029480.9, ENSMUST00000029480.9
    Conserved Domains (1) summary
    pfam03371
    Location:48 → 228
    PRP38; PRP38 family

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    108810121..108819055 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036163233.1 → XP_036019126.1  pre-mRNA-splicing factor 38B isoform X3

    Conserved Domains (1) summary
    TIGR01642
    Location:226 → 334
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

  2. XM_036163234.1 → XP_036019127.1  pre-mRNA-splicing factor 38B isoform X4

    Conserved Domains (1) summary
    TIGR01642
    Location:213 → 321
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

  3. XM_030252761.1 → XP_030108621.1  pre-mRNA-splicing factor 38B isoform X4

    Conserved Domains (1) summary
    TIGR01642
    Location:213 → 321
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor

  4. XM_006501914.3 → XP_006501977.1  pre-mRNA-splicing factor 38B isoform X1

    Conserved Domains (2) summary
    TIGR01642
    Location:299 → 407
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    pfam03371
    Location:15 → 116
    PRP38; PRP38 family

  5. XM_006501915.3 → XP_006501978.1  pre-mRNA-splicing factor 38B isoform X2

    Conserved Domains (2) summary
    TIGR01642
    Location:265 → 373
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
    pfam03371
    Location:1 → 82
    PRP38; PRP38 family

  6. XM_036163235.1 → XP_036019128.1  pre-mRNA-splicing factor 38B isoform X4

    Conserved Domains (1) summary
    TIGR01642
    Location:213 → 321
    U2AF_lg; U2 snRNP auxilliary factor, large subunit, splicing factor
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80SY5.1 GenPept UniProtKB/Swiss-Prot:Q80SY5

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