Prpf39 MGI Mouse Gene Detail - MGI:104602 - pre-mRNA processing factor 39

Symbol

Prpf39
Name

pre-mRNA processing factor 39
Synonyms

MGC:37077, Srcs1

Feature Type

protein coding gene
IDs

MGI:104602
NCBI Gene: 328110
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr12:65083107-65110160 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 27.21 cM
Mapping Data

1 experiment

SNPs within 2kb

688 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104602	protein coding gene	Chr12:65083094-65110160 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019778	protein coding gene	Chr12:64515693-64542741 (+)
A/J	MGP_AJ_G0019737	protein coding gene	Chr12:62134044-62161422 (+)
AKR/J	MGP_AKRJ_G0019712	protein coding gene	Chr12:64113728-64140780 (+)
BALB/cJ	MGP_BALBcJ_G0019717	protein coding gene	Chr12:62575747-62602838 (+)
C3H/HeJ	MGP_C3HHeJ_G0019522	protein coding gene	Chr12:64454945-64486885 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0020169	protein coding gene	Chr12:66552541-66579965 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017789	protein coding gene	Chr12:59950196-59977756 (+)
CAST/EiJ	MGP_CASTEiJ_G0019074	protein coding gene	Chr12:59162116-59193589 (+)
CBA/J	MGP_CBAJ_G0019491	protein coding gene	Chr12:68976420-69006185 (+)
DBA/2J	MGP_DBA2J_G0019607	protein coding gene	Chr12:62062427-62089528 (+)
FVB/NJ	MGP_FVBNJ_G0019595	protein coding gene	Chr12:61088509-61116000 (+)
LP/J	MGP_LPJ_G0019679	protein coding gene	Chr12:64534775-64564119 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019633	protein coding gene	Chr12:71840069-71873288 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020203	protein coding gene	Chr12:63501105-63528134 (+)
PWK/PhJ	MGP_PWKPhJ_G0018840	protein coding gene	Chr12:56334938-56362534 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0018634	protein coding gene	Chr12:57823219-57850989 (+)
WSB/EiJ	MGP_WSBEiJ_G0019125	protein coding gene	Chr12:64032574-64059612 (+)

Human Ortholog

PRPF39, pre-mRNA processing factor 39

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PRPF39, pre-mRNA processing factor 39
Links

HGNC:20314

NCBI Gene ID: 55015

neXtProt AC: NX_Q86UA1

UniProt: Q86UA1
Chr Location

14q21.2

MGI Vertebrate Homology

Prpf39 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PRPF39
Gene Tree

Prpf39

less

Phenotype Summary

9 phenotypes from 1 allele in 1 genetic background
10 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

14
Chemically induced (other)

1
Endonuclease-mediated

3
Gene trapped

8
Targeted

2
Genomic Mutations

1 involving Prpf39
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

50 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

less

All GO Annotations

8
GO References

3

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

less

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

706
cDNA Data

16
Literature Summary

1

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase prpf39, prpf39.2

less

All Sequences

69
RefSeq

10
UniProt

6
CCDS

CCDS25939.2

Ensembl

ENSMUSG00000035597 (Evidence)
NCBI Gene

328110

			Length	Strain/Species	Flank
genomic	ENSMUSG00000035597	Ensembl Gene Model \| MGI Sequence Detail	27054	C57BL/6J	± kb
transcript	ENSMUST00000120580	Ensembl \| MGI Sequence Detail	4069	Not Applicable
polypeptide	ENSMUSP00000112953	Ensembl \| MGI Sequence Detail	665	Not Applicable

less

UniProt

6 Sequences
Protein Ontology

PR:000013282 pre-mRNA-processing factor 39

(term hierarchy)
PDB

6G70
InterPro Domains

IPR003107 HAT (Half-A-TPR) repeat

IPR008847 Suppressor of forked

IPR011990 Tetratricopeptide-like helical domain superfamily
GlyGen

Q8K2Z2 3 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (1 site)

less

All nucleic 18

cDNA 18

Microarray probesets 6

less

MGD-MRK-26038

Summaries

All 35

Developmental Gene Expression 1

Gene Ontology 3

Phenotypes 10
Earliest

J:22534 Frankfort BJ, et al., Identification of novel cellular genes transcriptionally suppressed by v-src. Biochem Biophys Res Commun. 1995 Jan 26;206(3):916-26
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Prpf39:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr113600	Chr12:65083093-65083132 (+)	6 bp
Tssr113601	Chr12:65083601-65083607 (+)	497 bp
Tssr113602	Chr12:65086506-65086516 (+)	3,404 bp
Tssr113603	Chr12:65095962-65095972 (+)	12,860 bp
Tssr113604	Chr12:65108505-65108508 (+)	25,400 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/10/2024 MGI 6.24