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PRPF40A pre-mRNA processing factor 40 homolog A [ Homo sapiens (human) ]

Gene ID: 55660, updated on 6-Jan-2019

Summary

Official Symbol
PRPF40Aprovided by HGNC
Official Full Name
pre-mRNA processing factor 40 homolog Aprovided by HGNC
Primary source
HGNC:HGNC:16463
See related
Ensembl:ENSG00000196504 MIM:612941
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HYPA; FBP11; FLAF1; FNBP3; HIP10; Prp40; FBP-11; HIP-10; NY-REN-6
Expression
Ubiquitous expression in bone marrow (RPKM 15.6), testis (RPKM 13.4) and 25 other tissues See more
Orthologs

Genomic context

See PRPF40A in Genome Data Viewer
Location:
2q23.3
Exon count:
31
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (152651593..152718012, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (153508107..153574628, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene formin like 2 Neighboring gene nuclear distribution C pseudogene 1 Neighboring gene uncharacterized LOC105373690 Neighboring gene ADP ribosylation factor like GTPase 6 interacting protein 6 Neighboring gene ubiquilin 4 pseudogene 2 Neighboring gene uncharacterized LOC105373691

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify PRP40 pre-Mrna processing factor 40 homolog A (PRPF40A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify PRP40 pre-mRNA processing factor 40 homolog A (PRPF40A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify PRP40 pre-Mrna processing factor 40 homolog A (PRPF40A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify PRP40 pre-Mrna processing factor 40 homolog A (PRPF40A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20585

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA cis splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
regulation of cell shape IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cytokinesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
U1 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
pre-mRNA-processing factor 40 homolog A
Names
Fas-ligand associated factor 1
Huntingtin-interacting protein A
NY-REN-6 antigen
PRP40 pre-mRNA processing factor 40 homolog A
fas ligand-associated factor 1
formin binding protein 3
formin-binding protein 11
huntingtin yeast partner A
huntingtin-interacting protein 10
renal carcinoma antigen NY-REN-6

NCBI Reference Sequences (RefSeq)

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_001354431.1NP_001341360.1  pre-mRNA-processing factor 40 homolog A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:110751
    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 ...
  2. NM_001354432.1NP_001341361.1  pre-mRNA-processing factor 40 homolog A isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: TThis variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:38701
    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 ...
  3. NM_001365596.1NP_001352525.1  pre-mRNA-processing factor 40 homolog A isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:152815
    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 ...
  4. NM_001365597.1NP_001352526.1  pre-mRNA-processing factor 40 homolog A isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:152811
    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 ...
  5. NM_001365598.1NP_001352527.1  pre-mRNA-processing factor 40 homolog A isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:152797
    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 ...
  6. NM_001365599.1NP_001352528.1  pre-mRNA-processing factor 40 homolog A isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:152793
    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 ...
  7. NM_001365600.1NP_001352529.1  pre-mRNA-processing factor 40 homolog A isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:110773
    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 ...
  8. NM_001365601.1NP_001352530.1  pre-mRNA-processing factor 40 homolog A isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:110755
    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 ...
  9. NM_001365602.1NP_001352531.1  pre-mRNA-processing factor 40 homolog A isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:54717
    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 ...
  10. NM_001365603.1NP_001352532.1  pre-mRNA-processing factor 40 homolog A isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:54713
    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 ...
  11. NM_001365604.1NP_001352533.1  pre-mRNA-processing factor 40 homolog A isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:54695
    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 ...
  12. NM_001365605.1NP_001352534.1  pre-mRNA-processing factor 40 homolog A isoform 13

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    cl00157
    Location:54695
    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 ...
  13. NM_017892.4NP_060362.3  pre-mRNA-processing factor 40 homolog A isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS46430.1
    UniProtKB/Swiss-Prot
    O75400
    Related
    ENSP00000386458.2, ENST00000410080.6
    Conserved Domains (4) summary
    smart00441
    Location:717771
    FF; Contains two conserved F residues
    COG5104
    Location:110769
    PRP40; Splicing factor [RNA processing and modification]
    cd00201
    Location:119146
    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:368417
    FF; FF domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    152651593..152718012 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004459.2XP_016859948.1  pre-mRNA-processing factor 40 homolog A isoform X10

  2. XM_024452979.1XP_024308747.1  pre-mRNA-processing factor 40 homolog A isoform X12

    Conserved Domains (2) summary
    smart00441
    Location:617671
    FF; Contains two conserved F residues
    cl00157
    Location:6554
    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 ...
  3. XM_017004456.2XP_016859945.1  pre-mRNA-processing factor 40 homolog A isoform X8

    Conserved Domains (1) summary
    cl00157
    Location:54717
    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 ...
  4. XM_017004458.2XP_016859947.1  pre-mRNA-processing factor 40 homolog A isoform X10

  5. XM_011511449.3XP_011509751.1  pre-mRNA-processing factor 40 homolog A isoform X8

    Conserved Domains (1) summary
    cl00157
    Location:54717
    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 ...
  6. XM_017004453.2XP_016859942.1  pre-mRNA-processing factor 40 homolog A isoform X1

  7. XM_017004460.2XP_016859949.1  pre-mRNA-processing factor 40 homolog A isoform X11

    Conserved Domains (1) summary
    cl00157
    Location:54695
    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 ...
  8. XM_024452980.1XP_024308748.1  pre-mRNA-processing factor 40 homolog A isoform X13

    Conserved Domains (2) summary
    smart00441
    Location:613667
    FF; Contains two conserved F residues
    cl00157
    Location:6550
    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 ...
  9. XM_017004461.1XP_016859950.1  pre-mRNA-processing factor 40 homolog A isoform X11

    Conserved Domains (1) summary
    cl00157
    Location:54695
    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 ...
  10. XM_017004457.1XP_016859946.1  pre-mRNA-processing factor 40 homolog A isoform X9

    Conserved Domains (1) summary
    cl00157
    Location:54713
    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 ...
  11. XM_017004454.1XP_016859943.1  pre-mRNA-processing factor 40 homolog A isoform X4

  12. XM_005246676.4XP_005246733.3  pre-mRNA-processing factor 40 homolog A isoform X2

  13. XM_011511448.3XP_011509750.1  pre-mRNA-processing factor 40 homolog A isoform X7

    Conserved Domains (1) summary
    cl00157
    Location:110755
    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 ...
  14. XM_005246677.4XP_005246734.2  pre-mRNA-processing factor 40 homolog A isoform X6

    Conserved Domains (1) summary
    cl00157
    Location:110773
    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 ...
  15. XM_011511446.3XP_011509748.1  pre-mRNA-processing factor 40 homolog A isoform X3

    Conserved Domains (4) summary
    smart00441
    Location:809863
    FF; Contains two conserved F residues
    COG5104
    Location:216861
    PRP40; Splicing factor [RNA processing and modification]
    cd00201
    Location:225252
    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:456505
    FF; FF domain
  16. XM_011511447.3XP_011509749.1  pre-mRNA-processing factor 40 homolog A isoform X5

    Conserved Domains (4) summary
    smart00441
    Location:827881
    FF; Contains two conserved F residues
    COG5104
    Location:216879
    PRP40; Splicing factor [RNA processing and modification]
    cd00201
    Location:225252
    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:474523
    FF; FF domain
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