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FIP1L1 factor interacting with PAPOLA and CPSF1 [ Homo sapiens (human) ]

Gene ID: 81608, updated on 9-Jul-2017
Official Symbol
FIP1L1provided by HGNC
Official Full Name
factor interacting with PAPOLA and CPSF1provided by HGNC
Primary source
HGNC:HGNC:19124
See related
Ensembl:ENSG00000145216 MIM:607686; Vega:OTTHUMG00000128701
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Rhe; FIP1; hFip1
Summary
This gene encodes a subunit of the CPSF (cleavage and polyadenylation specificity factor) complex that polyadenylates the 3' end of mRNA precursors. This gene, the homolog of yeast Fip1 (factor interacting with PAP), binds to U-rich sequences of pre-mRNA and stimulates poly(A) polymerase activity. Its N-terminus contains a PAP-binding site and its C-terminus an RNA-binding domain. An interstitial chromosomal deletion on 4q12 creates an in-frame fusion of human genes FIP1L1 and PDGFRA (platelet-derived growth factor receptor, alpha). The FIP1L1-PDGFRA fusion gene encodes a constitutively activated tyrosine kinase that joins the first 233 amino acids of FIP1L1 to the last 523 amino acids of PDGFRA. This gene fusion and chromosomal deletion is the cause of some forms of idiopathic hypereosinophilic syndrome (HES). This syndrome, recently reclassified as chronic eosinophilic leukemia (CEL), is responsive to treatment with tyrosine kinase inhibitors. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
Orthologs
Location:
4q12
Exon count:
19
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 4 NC_000004.12 (53377572..53462611)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (54243803..54326103)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928658 Neighboring gene sec1 family domain containing 2 Neighboring gene RNA, U6 small nuclear 310, pseudogene Neighboring gene uncharacterized LOC105377654 Neighboring gene LNX1 antisense RNA 1 Neighboring gene ligand of numb-protein X 1 Neighboring gene COMM domain-containing protein 5-like

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
GWAS of DNA methylation variation within imprinting control regions suggests parent-of-origin association.
NHGRI GWA Catalog
Identification of a variant in KDR associated with serum VEGFR2 and pharmacodynamics of pazopanib.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify FIP1 like 1 protein (FIP1L1), 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 FIP1 like 1 protein (FIP1L1), 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 FIP1 like 1 protein (FIP1L1), 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 FIP1 like 1 protein (FIP1L1), 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

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • 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...
  • Processing of Capped Intronless Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intronless 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...
  • Processing of Intronless Pre-mRNAs, organism-specific biosystem (from REACTOME)
    Processing of Intronless Pre-mRNAs, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3' processing consists of two steps: The mRNA is first cleaved ...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing.
  • Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystemTransport of mature mRNAs derived from intronless transcripts require some of the same protein complexes as mRNAs derived from intron containing complexes, including TAP and Aly/Ref. However a number...
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • 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...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ33619, DKFZp586K0717

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA polyadenylation IBA
Inferred from Biological aspect of Ancestor
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
pre-mRNA cleavage required for polyadenylation IBA
Inferred from Biological aspect of Ancestor
more info
 
termination of RNA polymerase II transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
mRNA cleavage and polyadenylation specificity factor complex IBA
Inferred from Biological aspect of Ancestor
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
Preferred Names
pre-mRNA 3'-end-processing factor FIP1
Names
FIP1 like 1
FIP1-like 1 protein
FIP1L1 cleavage and polyadenylation specific factor subunit
factor interacting with PAP
rearranged in hypereosinophilia

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.

Genomic

  1. NG_008644.1 RefSeqGene

    Range
    5001..87284
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001134937.1NP_001128409.1  pre-mRNA 3'-end-processing factor FIP1 isoform 2

    See identical proteins and their annotated locations for NP_001128409.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region and has an additional in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC058822, AK295737, AY366510, DN990103
    Consensus CDS
    CCDS47055.1
    UniProtKB/Swiss-Prot
    Q6UN15
    Related
    ENSP00000351383.5, OTTHUMP00000218546, ENST00000358575.9, OTTHUMT00000361314
    Conserved Domains (1) summary
    pfam05182
    Location:139181
    Fip1; Fip1 motif
  2. NM_001134938.1NP_001128410.1  pre-mRNA 3'-end-processing factor FIP1 isoform 3

    See identical proteins and their annotated locations for NP_001128410.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC058822, AL136910, DN990103
    Consensus CDS
    CCDS47056.1
    UniProtKB/Swiss-Prot
    Q6UN15
    Related
    ENSP00000302993.6, OTTHUMP00000218547, ENST00000306932.10, OTTHUMT00000361315
    Conserved Domains (1) summary
    pfam05182
    Location:139181
    Fip1; Fip1 motif
  3. NM_030917.3NP_112179.2  pre-mRNA 3'-end-processing factor FIP1 isoform 1

    See identical proteins and their annotated locations for NP_112179.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC058822, AY366510, DN990103
    Consensus CDS
    CCDS3491.1
    UniProtKB/Swiss-Prot
    Q6UN15
    Related
    ENSP00000336752.6, OTTHUMP00000158885, ENST00000337488.10, OTTHUMT00000250602
    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p7 Primary Assembly

    Range
    53377572..53462611
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008668.1XP_016864157.1  pre-mRNA 3'-end-processing factor FIP1 isoform X13

  2. XM_017008664.1XP_016864153.1  pre-mRNA 3'-end-processing factor FIP1 isoform X6

    Conserved Domains (1) summary
    pfam05182
    Location:139181
    Fip1; Fip1 motif
  3. XM_005265773.4XP_005265830.1  pre-mRNA 3'-end-processing factor FIP1 isoform X2

    See identical proteins and their annotated locations for XP_005265830.1

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  4. XM_005265769.4XP_005265826.1  pre-mRNA 3'-end-processing factor FIP1 isoform X1

    See identical proteins and their annotated locations for XP_005265826.1

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  5. XM_005265781.4XP_005265838.1  pre-mRNA 3'-end-processing factor FIP1 isoform X12

    See identical proteins and their annotated locations for XP_005265838.1

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  6. XM_005265778.4XP_005265835.1  pre-mRNA 3'-end-processing factor FIP1 isoform X8

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  7. XM_017008666.1XP_016864155.1  pre-mRNA 3'-end-processing factor FIP1 isoform X9

  8. XM_017008669.1XP_016864158.1  pre-mRNA 3'-end-processing factor FIP1 isoform X15

    Conserved Domains (1) summary
    pfam05182
    Location:139181
    Fip1; Fip1 motif
  9. XM_017008662.1XP_016864151.1  pre-mRNA 3'-end-processing factor FIP1 isoform X3

    Conserved Domains (1) summary
    pfam05182
    Location:139181
    Fip1; Fip1 motif
  10. XM_017008663.1XP_016864152.1  pre-mRNA 3'-end-processing factor FIP1 isoform X5

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  11. XM_005265774.4XP_005265831.1  pre-mRNA 3'-end-processing factor FIP1 isoform X4

    See identical proteins and their annotated locations for XP_005265831.1

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  12. XM_017008667.1XP_016864156.1  pre-mRNA 3'-end-processing factor FIP1 isoform X10

    Conserved Domains (1) summary
    pfam05182
    Location:139181
    Fip1; Fip1 motif
  13. XM_005265779.4XP_005265836.1  pre-mRNA 3'-end-processing factor FIP1 isoform X11

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  14. XM_017008670.1XP_016864159.1  pre-mRNA 3'-end-processing factor FIP1 isoform X16

  15. XM_017008671.1XP_016864160.1  pre-mRNA 3'-end-processing factor FIP1 isoform X17

  16. XM_017008665.1XP_016864154.1  pre-mRNA 3'-end-processing factor FIP1 isoform X7

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif
  17. XM_005265782.4XP_005265839.1  pre-mRNA 3'-end-processing factor FIP1 isoform X14

    See identical proteins and their annotated locations for XP_005265839.1

    Conserved Domains (1) summary
    pfam05182
    Location:154196
    Fip1; Fip1 motif

Alternate CHM1_1.1

Genomic

  1. NC_018915.2 Alternate CHM1_1.1

    Range
    54279549..54361766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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