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Prpf39 pre-mRNA processing factor 39 [ Mus musculus (house mouse) ]

Gene ID: 328110, updated on 8-Feb-2024

Summary

Official Symbol
Prpf39provided by MGI
Official Full Name
pre-mRNA processing factor 39provided by MGI
Primary source
MGI:MGI:104602
See related
Ensembl:ENSMUSG00000035597 AllianceGenome:MGI:104602
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
Srcs1
Summary
Predicted to be involved in mRNA 5'-splice site recognition. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex. Orthologous to human PRPF39 (pre-mRNA processing factor 39). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E18 (RPKM 13.3), CNS E11.5 (RPKM 12.7) and 25 other tissues See more
Orthologs
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Genomic context

See Prpf39 in Genome Data Viewer
Location:
12 C1; 12 27.21 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (65083094..65110160)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (65036334..65063386)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene kelch-like 28 Neighboring gene TOG array regulator of axonemal microtubules 1 Neighboring gene STARR-seq mESC enhancer starr_32311 Neighboring gene STARR-positive B cell enhancer ABC_E7138 Neighboring gene predicted gene, 51966 Neighboring gene STARR-seq mESC enhancer starr_32313 Neighboring gene predicted gene, 25970 Neighboring gene STARR-positive B cell enhancer ABC_E5331 Neighboring gene STARR-positive B cell enhancer ABC_E4026 Neighboring gene FK506 binding protein 3 Neighboring gene Fanconi anemia, complementation group M Neighboring gene STARR-seq mESC enhancer starr_32318 Neighboring gene MIS18 binding protein 1 Neighboring gene STARR-seq mESC enhancer starr_32320

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 

General gene information

Markers

Clone Names

  • FLJ11128, MGC37077

Gene Ontology Provided by MGI

Function Evidence Code Pubs
contributes_to pre-mRNA 5'-splice site binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA 5'-splice site recognition IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of U1 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of commitment complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
pre-mRNA-processing factor 39
Names
PRP39 homolog
PRP39 pre-mRNA processing factor 39 homolog
v-src suppressed transcript 1

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_001374212.1NP_001361141.1  pre-mRNA-processing factor 39 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC159621
    Conserved Domains (2) summary
    COG5107
    Location:40419
    RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
    sd00006
    Location:334362
    TPR; TPR repeat [structural motif]
  2. NM_001374213.1NP_001361142.1  pre-mRNA-processing factor 39 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC159621
    Conserved Domains (2) summary
    COG5107
    Location:40419
    RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
    sd00006
    Location:334362
    TPR; TPR repeat [structural motif]
  3. NM_177806.3NP_808474.2  pre-mRNA-processing factor 39 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AI790078, AK168462, BC076622, BY069337
    Consensus CDS
    CCDS25939.2
    UniProtKB/Swiss-Prot
    Q8C1I4, Q8K2Z2
    UniProtKB/TrEMBL
    E9QJV4
    Related
    ENSMUSP00000112953.2, ENSMUST00000120580.8
    Conserved Domains (2) summary
    COG5107
    Location:68538
    RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]
    sd00006
    Location:453481
    TPR; TPR repeat [structural motif]

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    65083094..65110160
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006516029.4XP_006516092.1  pre-mRNA-processing factor 39 isoform X1

    Conserved Domains (1) summary
    smart00386
    Location:166198
    HAT; HAT (Half-A-TPR) repeats

RNA

  1. XR_001780462.3 RNA Sequence

    Related
    ENSMUST00000129956.2
  2. XR_004937522.1 RNA Sequence