Prpf40a MGI Mouse Gene Detail - MGI:1860512 - pre-mRNA processing factor 40A

Symbol

Prpf40a
Name

pre-mRNA processing factor 40A
Synonyms

2810012K09Rik, FBP11, Fnbp3

Feature Type

protein coding gene
IDs

MGI:1860512
NCBI Gene: 56194
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr2:53024714-53081450 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 30.69 cM, cytoband C1
Mapping Data

3 experiments

SNPs within 2kb

1219 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1860512	protein coding gene	Chr2:53024714-53081714 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0025738	protein coding gene	Chr2:52523342-52580917 (-)
A/J	MGP_AJ_G0025714	protein coding gene	Chr2:50481373-50537730 (-)
AKR/J	MGP_AKRJ_G0025684	protein coding gene	Chr2:51926357-51984258 (-)
BALB/cJ	MGP_BALBcJ_G0025709	protein coding gene	Chr2:50586233-50643061 (-)
C3H/HeJ	MGP_C3HHeJ_G0025470	protein coding gene	Chr2:51950759-52007902 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0026155	protein coding gene	Chr2:54048059-54106173 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023561	protein coding gene	Chr2:48451286-48506697 (-)
CAST/EiJ	MGP_CASTEiJ_G0024935	protein coding gene	Chr2:52068813-52125047 (-)
CBA/J	MGP_CBAJ_G0025450	protein coding gene	Chr2:56105272-56167006 (-)
DBA/2J	MGP_DBA2J_G0025581	protein coding gene	Chr2:50127662-50185168 (-)
FVB/NJ	MGP_FVBNJ_G0025543	protein coding gene	Chr2:49814471-49870814 (-)
LP/J	MGP_LPJ_G0025669	protein coding gene	Chr2:52423613-52484437 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025574	protein coding gene	Chr2:57102252-57167343 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026213	protein coding gene	Chr2:51860874-51917501 (-)
PWK/PhJ	MGP_PWKPhJ_G0024676	protein coding gene	Chr2:50016737-50073769 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0024482	protein coding gene	Chr2:52090276-52147852 (-)
WSB/EiJ	MGP_WSBEiJ_G0025002	protein coding gene	Chr2:52150302-52204947 (-)

Human Ortholog

PRPF40A, pre-mRNA processing factor 40 homolog A

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PRPF40A, pre-mRNA processing factor 40 homolog A
Synonyms

FBP-11, FBP11, FLAF1, FNBP3, HIP-10, HIP10, HYPA, NY-REN-6, Prp40
Links

HGNC:16463

NCBI Gene ID: 55660

neXtProt AC: NX_O75400

UniProt: O75400
Chr Location

2q23.3; chr2:152651593-152718019 (-) GRCh38

MGI Vertebrate Homology

Prpf40a stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PRPF40A
Gene Tree

Prpf40a

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Phenotype Summary

9 phenotypes from 1 allele in 1 genetic background
12 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

32
Chemically induced (other)

1
Endonuclease-mediated

4
Gene trapped

27
Genomic Mutations

1 involving Prpf40a
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

62 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

20
GO References

9

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.

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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

844
Tissues

124
cDNA Data

15
Literature Summary

3

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

GEO

Expression Atlas
Other Vertebrate Links

Xenbase prpf40a

ZFIN prpf40a

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All Sequences

89
RefSeq

20
UniProt

9
CCDS

CCDS16038.1, CCDS89487.1

Ensembl

ENSMUSG00000061136 (Evidence)
NCBI Gene

56194

			Length	Strain/Species	Flank
genomic	56194	NCBI Gene Model \| MGI Sequence Detail	56737	C57BL/6J	± kb
transcript	NM_001371015	RefSeq \| MGI Sequence Detail	7417	C57BL/6
polypeptide	Q9R1C7	UniProt \| EBI \| MGI Sequence Detail	953	Not Applicable

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UniProt

9 Sequences
Protein Ontology

PR:000013284 pre-mRNA-processing factor 40 homolog A

(term hierarchy)
InterPro Domains

IPR002713 FF domain

IPR036517 FF domain superfamily

IPR039726 Pre-mRNA-processing factor Prp40

IPR001202 WW domain

IPR036020 WW domain superfamily
GlyGen

Q9R1C7 1 site, 1 O-linked glycan (1 site)

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All nucleic 19

cDNA 17

Primer pair 1

Other 1

Microarray probesets 10

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MGI:1922669

Summaries

All 47

Developmental Gene Expression 3

Gene Ontology 9

Phenotypes 12
Earliest

J:38792 Chan DC, et al., Formin binding proteins bear WWP/WW domains that bind proline-rich peptides and functionally resemble SH3 domains. EMBO J. 1996 Mar 1;15(5):1045-54
Latest

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

TSS for Prpf40a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr24102	Chr2:53081982-53081997 (-)	-540 bp
Tssr24101	Chr2:53081226-53081272 (-)	201 bp
Tssr24100	Chr2:53081207-53081221 (-)	236 bp
Tssr24099	Chr2:53080825-53080857 (-)	609 bp
Tssr24098	Chr2:53043090-53043107 (-)	38,351 bp
Tssr24097	Chr2:53036151-53036168 (-)	45,290 bp
Tssr24096	Chr2:53035911-53035936 (-)	45,526 bp
Tssr24095	Chr2:53035362-53035388 (-)	46,075 bp
Tssr24094	Chr2:53028119-53028132 (-)	53,324 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)
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