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PPFIA4 PTPRF interacting protein alpha 4 [ Homo sapiens (human) ]

Gene ID: 8497, updated on 2-Nov-2024

Summary

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Official Symbol
PPFIA4provided by HGNC
Official Full Name
PTPRF interacting protein alpha 4provided by HGNC
Primary source
HGNC:HGNC:9248
See related
Ensembl:ENSG00000143847 MIM:603145; AllianceGenome:HGNC:9248
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
Summary
PPFIA4, or liprin-alpha-4, belongs to the liprin-alpha gene family. See liprin-alpha-1 (LIP1, or PPFIA1; MIM 611054) for background on liprins.[supplied by OMIM, Mar 2008]
Expression
Biased expression in brain (RPKM 8.9), heart (RPKM 8.4) and 10 other tissues See more
Orthologs
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Genomic context

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See PPFIA4 in Genome Data Viewer
Location:
1q32.1
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (203026491..203078736)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (202289215..202341489)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202995619..203047864)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MGAT4 family member F, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr1.10803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202975854-202976628 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202976629-202977401 Neighboring gene ribosomal protein S20 pseudogene 8 Neighboring gene transmembrane protein 183A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202995545-202996066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203010223-203010724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203010725-203011224 Neighboring gene Sharpr-MPRA regulatory region 9252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203013943-203014581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203014582-203015219 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203015372-203015574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203017091-203017988 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203020635-203021176 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:203023677-203024428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203024429-203025180 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:203030137-203030721 Neighboring gene uncharacterized LOC105371687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203044947-203045682 Neighboring gene NANOG hESC enhancer GRCh37_chr1:203056459-203056976 Neighboring gene myogenin promoter associated myogenic regulatory antisense long non coding RNA Neighboring gene myogenin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203096578-203097558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203103311-203104198 Neighboring gene adenosine A1 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203112572-203113072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203114546-203115227 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203134798-203134977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203135305-203135815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203135816-203136326

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PPFIA4 Promotes Proliferation, Migration and Glycolysis of Esophageal Cancer Cells.
    Title: PPFIA4 Promotes Proliferation, Migration and Glycolysis of Esophageal Cancer Cells.
  2. Hypoxia appears to up-regulate the expression of liprin-alpha4, which induces the expression of HIF1alpha. HIF1alpha contributes to increased proliferation and lower chemosensitivity. Therefore, inhibition of liprin-alpha4 or HIF1alpha led to reduced proliferation and increased chemosensitivity of SBC-5 cells.
    Title: Liprin-α4 as a New Therapeutic Target for SCLC as an Upstream Mediator of HIF1α.
  3. The results identify PP1IFA4 loci associated with early onset atrial fibrillation in a Korean population.
    Title: Korean atrial fibrillation network genome-wide association study for early-onset atrial fibrillation identifies novel susceptibility loci.
  4. Data show that liprin-alpha4 plays a pivotal role in inducing malignant phenotypes such as increased proliferation and invasion in pancreatic cancer, and that liprin-alpha4 could be a new effective therapeutic target for pancreatic cancer.
    Title: Liprin-α4 as a Possible New Therapeutic Target for Pancreatic Cancer.
  5. presence of Liprin-alpha4 and nickel increased tyrosine phosphatase activity that reduced the global levels of tyrosine phosphorylation in the cell
    Title: Liprin-α4 is required for nickel induced receptor protein tyrosine phosphatase-leukocyte antigen related receptor F (RPTP-LAR) activity.
  6. liprin-alpha4 is a hypoxia-induced gene potentially involved in cell-cell adhesion
    Title: Liprin-α4 is a new hypoxia-inducible target gene required for maintenance of cell-cell contacts.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in synapse organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cell surface IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in presynaptic active zone IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in presynaptic active zone TAS
Traceable Author Statement
more info
 PubMed 
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
liprin-alpha-4
Names
protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4

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_001304331.2 → NP_001291260.1  liprin-alpha-4 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB020704, AC096632, AC105940, AK295757, AL540093, DA327222, EF428334
    Consensus CDS
    CCDS91145.1
    UniProtKB/TrEMBL
    A0A8J8YUZ5, B1APN9
    Related
    ENSP00000295706.5, ENST00000295706.9
    Conserved Domains (5) summary
    cd09562
    Location:848 → 918
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:965 → 1030
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:1050 → 1121
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    smart00454
    Location:848 → 914
    SAM; Sterile alpha motif
    cl02488
    Location:338 → 493
    SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

  2. NM_001304332.2 → NP_001291261.1  liprin-alpha-4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC096632, AC105940, AK023365, AK295757, AL540093, BC144262, DA327222, EF428334
    UniProtKB/TrEMBL
    B1APN9
    Conserved Domains (5) summary
    cd09562
    Location:848 → 918
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:956 → 1021
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:1041 → 1112
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    COG0419
    Location:25 → 490
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    COG1196
    Location:262 → 491
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  3. NM_001393950.1 → NP_001380879.1  liprin-alpha-4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    B1APN9
    Conserved Domains (4) summary
    cd09562
    Location:839 → 909
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:956 → 1021
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:1041 → 1112
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    COG1196
    Location:161 → 484
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  4. NM_001393951.1 → NP_001380880.1  liprin-alpha-4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    A0A8I5QJ45
    Related
    ENSP00000508419.1, ENST00000692772.1
    Conserved Domains (5) summary
    cd09562
    Location:827 → 897
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:944 → 1009
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:1029 → 1100
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    COG0419
    Location:36 → 470
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    COG1196
    Location:262 → 470
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

  5. NM_001393952.1 → NP_001380881.1  liprin-alpha-4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    B1APN9
    Conserved Domains (5) summary
    cd09562
    Location:848 → 918
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:965 → 1030
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    COG0419
    Location:25 → 490
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    COG1196
    Location:262 → 491
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cl15755
    Location:1050 → 1108
    SAM_superfamily; SAM (Sterile alpha motif )

  6. NM_001393953.1 → NP_001380882.1  liprin-alpha-4 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    A0A8I5QJ45
    Conserved Domains (5) summary
    cd09562
    Location:803 → 873
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:920 → 985
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:1005 → 1076
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    COG1196
    Location:161 → 448
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam15921
    Location:21 → 615
    CCDC158; Coiled-coil domain-containing protein 158

  7. NM_001393954.1 → NP_001380883.1  liprin-alpha-4 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    B1APN9
    Conserved Domains (5) summary
    cd09562
    Location:803 → 873
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:920 → 985
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:1005 → 1076
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    COG1196
    Location:161 → 448
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam15921
    Location:21 → 615
    CCDC158; Coiled-coil domain-containing protein 158

  8. NM_001393955.1 → NP_001380884.1  liprin-alpha-4 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    A0A8I5QJ45
    Conserved Domains (5) summary
    cd09562
    Location:782 → 852
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:899 → 964
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:984 → 1055
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    TIGR02168
    Location:147 → 424
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam15921
    Location:21 → 594
    CCDC158; Coiled-coil domain-containing protein 158

  9. NM_001393956.1 → NP_001380885.1  liprin-alpha-4 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    B1APN9
    Conserved Domains (5) summary
    cd09562
    Location:782 → 852
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:890 → 955
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:975 → 1046
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    TIGR02168
    Location:147 → 424
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam15921
    Location:21 → 594
    CCDC158; Coiled-coil domain-containing protein 158

  10. NM_001393957.1 → NP_001380886.1  liprin-alpha-4 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC096632, AC105940, AL451082
    UniProtKB/TrEMBL
    A0A8I5QJ45
    Conserved Domains (5) summary
    cd09562
    Location:759 → 829
    SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
    cd09565
    Location:876 → 941
    SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
    cd09568
    Location:961 → 1032
    SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
    COG1196
    Location:145 → 404
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam15921
    Location:21 → 571
    CCDC158; Coiled-coil domain-containing protein 158

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    203026491..203078736
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    202289215..202341489
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_015053.1: Suppressed sequence

    Description
    NM_015053.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75335.3 GenPept UniProtKB/Swiss-Prot:O75335

Gene LinkOut

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