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

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 contribute to pre-mRNA 5'-splice site binding activity. Predicted to be involved in mRNA 5'-splice site recognition. 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, Nov 2024]
Expression: Broad expression in CNS E18 (RPKM 13.3), CNS E11.5 (RPKM 12.7) and 25 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000078.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

organisms with higher splicing complexity have substituted the Prp39/Prp42 heterodimer with a PRPF39 homodimer
Title: Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39.

Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)

General gene information

Go to the top of the page Help

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 splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA 5'-splice site recognition	IBA Inferred from Biological aspect of Ancestor more info
involved_in 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

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

NM_001374212.1 → NP_001361141.1 pre-mRNA-processing factor 39 isoform 2

Status: VALIDATED

Source sequence(s)

AC159621

Conserved Domains (2) summary

COG5107
Location:40 → 419

RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

sd00006
Location:334 → 362

TPR; TPR repeat [structural motif]
NM_001374213.1 → NP_001361142.1 pre-mRNA-processing factor 39 isoform 2

Status: VALIDATED

Source sequence(s)

AC159621

Conserved Domains (2) summary

COG5107
Location:40 → 419

RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

sd00006
Location:334 → 362

TPR; TPR repeat [structural motif]
NM_177806.3 → NP_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:68 → 538

RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

sd00006
Location:453 → 481

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

NC_000078.7 Reference GRCm39 C57BL/6J

Range

65083094..65110160

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

smart00386
Location:166 → 198

HAT; HAT (Half-A-TPR) repeats