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

Gene ID: 55660, updated on 21-Dec-2022

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; AllianceGenome:HGNC:16463
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
Summary
Enables RNA binding activity. Involved in several processes, including cytoskeleton organization; regulation of cell shape; and regulation of cytokinesis. Located in nuclear matrix and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 15.6), testis (RPKM 13.4) and 25 other tissues See more
Orthologs
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Genomic context

See PRPF40A in Genome Data Viewer
Location:
2q23.3
Exon count:
29
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (152651732..152718019, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (153104294..153170565, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (153508246..153574533, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene formin like 2 Neighboring gene Sharpr-MPRA regulatory region 469 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:153309665-153310256 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 Functions

What'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 PubChem

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
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in cell division IEA
Inferred from Electronic Annotation
more info
 
involved_in cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
involved_in regulation of cell shape IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of cytokinesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of U1 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in membrane HDA PubMed 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in 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)

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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)

  1. NM_001354431.4NP_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
    COG5104
    Location:110751
    PRP40; Splicing factor [RNA processing and modification]
  2. NM_001354432.4NP_001341361.1  pre-mRNA-processing factor 40 homolog A isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This 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_001365596.4NP_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_001365597.4NP_001352526.1  pre-mRNA-processing factor 40 homolog A isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS92876.1
    UniProtKB/TrEMBL
    F5H578
    Related
    ENSP00000444656.4, ENST00000545856.8
    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_001365598.4NP_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_001365599.4NP_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_001365600.4NP_001352529.1  pre-mRNA-processing factor 40 homolog A isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS92878.1
    UniProtKB/TrEMBL
    A0A8V8TM61
    Related
    ENSP00000513920.1, ENST00000698772.1
    Conserved Domains (1) summary
    COG5104
    Location:110773
    PRP40; Splicing factor [RNA processing and modification]
  8. NM_001365601.4NP_001352530.1  pre-mRNA-processing factor 40 homolog A isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:110755
    PRP40; Splicing factor [RNA processing and modification]
  9. NM_001365602.4NP_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_001365603.4NP_001352532.1  pre-mRNA-processing factor 40 homolog A isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:54713
    PRP40; Splicing factor [RNA processing and modification]
  11. NM_001365604.4NP_001352533.1  pre-mRNA-processing factor 40 homolog A isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:54695
    PRP40; Splicing factor [RNA processing and modification]
  12. NM_001365605.4NP_001352534.1  pre-mRNA-processing factor 40 homolog A isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:54695
    PRP40; Splicing factor [RNA processing and modification]
  13. NM_001395472.1NP_001382401.1  pre-mRNA-processing factor 40 homolog A isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS92878.1
    UniProtKB/TrEMBL
    A0A8V8TM61
    Conserved Domains (1) summary
    COG5104
    Location:110773
    PRP40; Splicing factor [RNA processing and modification]
  14. NM_001395473.1NP_001382402.1  pre-mRNA-processing factor 40 homolog A isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:110769
    PRP40; Splicing factor [RNA processing and modification]
  15. NM_001395475.1NP_001382404.1  pre-mRNA-processing factor 40 homolog A isoform 13

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:95758
    PRP40; Splicing factor [RNA processing and modification]
  16. NM_001395476.1NP_001382405.1  pre-mRNA-processing factor 40 homolog A isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:110755
    PRP40; Splicing factor [RNA processing and modification]
  17. NM_001395477.1NP_001382406.1  pre-mRNA-processing factor 40 homolog A isoform 14

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS92877.1
    UniProtKB/TrEMBL
    A0A8Q3SIG7
    Related
    ENSP00000512592.1, ENST00000696382.1
    Conserved Domains (1) summary
    COG5104
    Location:95754
    PRP40; Splicing factor [RNA processing and modification]
  18. NM_001395478.1NP_001382407.1  pre-mRNA-processing factor 40 homolog A isoform 14

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS92877.1
    UniProtKB/TrEMBL
    A0A8Q3SIG7
    Conserved Domains (1) summary
    COG5104
    Location:95754
    PRP40; Splicing factor [RNA processing and modification]
  19. NM_001395479.1NP_001382408.1  pre-mRNA-processing factor 40 homolog A isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:110751
    PRP40; Splicing factor [RNA processing and modification]
  20. NM_001395480.1NP_001382409.1  pre-mRNA-processing factor 40 homolog A isoform 15

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (3) summary
    PHA03255
    Location:165307
    PHA03255; BDLF3; Provisional
    COG5104
    Location:298716
    PRP40; Splicing factor [RNA processing and modification]
    cd00201
    Location:104134
    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 ...
  21. NM_001395481.1NP_001382410.1  pre-mRNA-processing factor 40 homolog A isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:54713
    PRP40; Splicing factor [RNA processing and modification]
  22. NM_001395482.1NP_001382411.1  pre-mRNA-processing factor 40 homolog A isoform 16

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (1) summary
    COG5104
    Location:54699
    PRP40; Splicing factor [RNA processing and modification]
  23. NM_001395483.1NP_001382412.1  pre-mRNA-processing factor 40 homolog A isoform 17

    Status: VALIDATED

    Source sequence(s)
    AC012443, AC079344
    Conserved Domains (2) summary
    smart00441
    Location:617671
    FF; Contains two conserved F residues
    COG5104
    Location:6554
    PRP40; Splicing factor [RNA processing and modification]
  24. NM_001395488.1NP_001382417.1  pre-mRNA-processing factor 40 homolog A isoform 18

    Status: VALIDATED

    Description
    Transcript Variant: This variant (25) encodes the longest isoform (18).
    Source sequence(s)
    AC012443, AC079344
    Consensus CDS
    CCDS92879.1
    UniProtKB/TrEMBL
    A0A7N4I394
    Related
    ENSP00000386458.4, ENST00000410080.8
    Conserved Domains (1) summary
    COG5104
    Location:174833
    PRP40; Splicing factor [RNA processing and modification]
  25. NM_017892.5NP_060362.3  pre-mRNA-processing factor 40 homolog A isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC012443, AC079344
    UniProtKB/Swiss-Prot
    O75400
    Conserved Domains (1) summary
    COG5104
    Location:110769
    PRP40; Splicing factor [RNA processing and modification]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    152651732..152718019 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444942.1XP_047300898.1  pre-mRNA-processing factor 40 homolog A isoform X3

  2. XM_047444941.1XP_047300897.1  pre-mRNA-processing factor 40 homolog A isoform X2

    Related
    ENSP00000513921.1, ENST00000698773.1
  3. XM_011511447.4XP_011509749.2  pre-mRNA-processing factor 40 homolog A isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    153104294..153170565 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)