Prpf40a pre-mRNA processing factor 40 homolog A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Prpf40aprovided by RGD
Official Full Name: pre-mRNA processing factor 40 homolog Aprovided by RGD
Primary source: RGD:1311401
See related: EnsemblRapid:ENSRNOG00000004864 AllianceGenome:RGD:1311401
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Fnbp3
Summary: Predicted to enable RNA binding activity and proline-rich region binding activity. Predicted to be involved in several processes, including mRNA splicing, via spliceosome; regulation of cell shape; and regulation of cytokinesis. Predicted to be located in nuclear matrix and nuclear speck. Predicted to be part of U1 snRNP and U2-type prespliceosome. Orthologous to human PRPF40A (pre-mRNA processing factor 40 homolog A). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 266.3), Spleen (RPKM 229.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q12

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (58036779..58098996, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (37625585..37689859, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (38680583..38741570, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Prpf40a (e-PCR), detects polymorphism
- UniSTS:507180

AI461736 (e-PCR)
- UniSTS:165168

RH133617 (e-PCR)
- UniSTS:216900

RH140784 (e-PCR)
- UniSTS:222850

UniSTS:234392 (e-PCR)
- UniSTS:234392

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables proline-rich region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell migration	ISO Inferred from Sequence Orthology more info
involved_in cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytokinesis	ISO Inferred from Sequence Orthology 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
located_in nuclear matrix	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: pre-mRNA-processing factor 40 homolog A

Names: PRP40 pre-mRNA processing factor 40 homolog A; formin binding protein 3

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)

NM_001106480.1 → NP_001099950.1 pre-mRNA-processing factor 40 homolog A

See identical proteins and their annotated locations for NP_001099950.1

Status: PROVISIONAL

Source sequence(s)

CH473983

UniProtKB/TrEMBL

A0A8I5ZVY5, A6JF33

Related

ENSRNOP00000107993.1, ENSRNOT00000128758.1

Conserved Domains (4) summary

smart00441
Location:740 → 794

FF; Contains two conserved F residues

COG5104
Location:146 → 677

PRP40; Splicing factor [RNA processing and modification]

cd00201
Location:146 → 173

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:391 → 440

FF; FF domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086021.1 Reference GRCr8

Range

58036779..58098996 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039104476.2 → XP_038960404.1 pre-mRNA-processing factor 40 homolog A isoform X6

UniProtKB/TrEMBL

A0A8I5ZVY5
XM_008761712.4 → XP_008759934.1 pre-mRNA-processing factor 40 homolog A isoform X5

UniProtKB/TrEMBL

A0A8I5ZVY5

Conserved Domains (3) summary

smart00441
Location:761 → 815

FF; Contains two conserved F residues

cd00201
Location:181 → 208

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:408 → 457

FF; FF domain
XM_008761711.4 → XP_008759933.1 pre-mRNA-processing factor 40 homolog A isoform X3

UniProtKB/TrEMBL

A0A8I5ZVI3, A0A8I5ZVY5

Conserved Domains (3) summary

smart00441
Location:779 → 833

FF; Contains two conserved F residues

cd00201
Location:181 → 208

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:426 → 475

FF; FF domain
XM_039104475.2 → XP_038960403.1 pre-mRNA-processing factor 40 homolog A isoform X2

UniProtKB/TrEMBL

A0A8I5ZVY5
XM_008761710.4 → XP_008759932.1 pre-mRNA-processing factor 40 homolog A isoform X1

UniProtKB/TrEMBL

A0A8I5ZVY5

Related

ENSRNOP00000083490.2, ENSRNOT00000095713.2

Conserved Domains (3) summary

smart00441
Location:803 → 857

FF; Contains two conserved F residues

cd00201
Location:223 → 250

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:450 → 499

FF; FF domain
XM_008761709.4 → XP_008759931.1 pre-mRNA-processing factor 40 homolog A isoform X8

UniProtKB/TrEMBL

A0A8I5ZVY5

Conserved Domains (3) summary

smart00441
Location:821 → 875

FF; Contains two conserved F residues

cd00201
Location:223 → 250

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:468 → 517

FF; FF domain
XM_063283248.1 → XP_063139318.1 pre-mRNA-processing factor 40 homolog A isoform X7

UniProtKB/TrEMBL

A0A8I5ZVY5
XM_006234164.5 → XP_006234226.1 pre-mRNA-processing factor 40 homolog A isoform X4

UniProtKB/TrEMBL

A0A8I5ZVY5

Conserved Domains (4) summary

smart00441
Location:775 → 829

FF; Contains two conserved F residues

COG5104
Location:181 → 712

PRP40; Splicing factor [RNA processing and modification]

cd00201
Location:181 → 208

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:426 → 475

FF; FF domain
XM_008761713.4 → XP_008759935.1 pre-mRNA-processing factor 40 homolog A isoform X9

UniProtKB/TrEMBL

A0A8I5ZVY5

Related

ENSRNOP00000083163.2, ENSRNOT00000104801.2

Conserved Domains (4) summary

smart00441
Location:661 → 715

FF; Contains two conserved F residues

COG5104
Location:63 → 598

PRP40; Splicing factor [RNA processing and modification]

cd00201
Location:63 → 90

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam01846
Location:308 → 357

FF; FF domain
XM_063283249.1 → XP_063139319.1 pre-mRNA-processing factor 40 homolog A isoform X10