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    RAPH1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 [ Homo sapiens (human) ]

    Gene ID: 65059, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RAPH1provided by HGNC
    Official Full Name
    Ras association (RalGDS/AF-6) and pleckstrin homology domains 1provided by HGNC
    Primary source
    HGNC:HGNC:14436
    See related
    Ensembl:ENSG00000173166 MIM:609035; AllianceGenome:HGNC:14436
    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
    LPD; RMO1; PREL2; PREL-2; ALS2CR9; ALS2CR18; RalGDS/AF-6
    Summary
    This gene encodes a protein that belongs to the Mig10/Rap1-interacting adaptor molecule/Lamellipodin family of adapter proteins, which function in cell migration. Members of this family contain pleckstrin-homology domains, Ras-association domains, and proline-rich C-termini. The protein encoded by this gene regulates actin dynamics through interaction with Ena/Vasodilator proteins as well as direct binding to filamentous actin to regulate actin network assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 14.2), liver (RPKM 12.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAPH1 in Genome Data Viewer
    Location:
    2q33.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (203433682..203535301, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (203915590..204017213, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (204298405..204400024, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:204192004-204192974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12255 Neighboring gene mitochondrial ribosomal protein L50 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:204209822-204210322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17011 Neighboring gene MPRA-validated peak4020 silencer Neighboring gene abl interactor 2 Neighboring gene tRNA-Glu (anticodon TTC) 9-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12258 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:204464991-204465874 Neighboring gene zinc finger protein 207 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:204530085-204530727 Neighboring gene NDUFA4, mitochondrial complex associated pseudogene

    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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    Related articles in PubMed

    1. Association between RAPH1 Gene Haplotypes and CHE2 Locus Phenotypes. A De Andrade F, et al. Ann Hum Genet, 2016 Jul. PMID 27346732
    2. Mechanistic insights into the phosphatidylinositol binding properties of the pleckstrin homology domain of lamellipodin. Gorai S, et al. Mol Biosyst, 2016 Mar. PMID 26726010
    3. Lamellipodin Is Important for Cell-to-Cell Spread and Actin-Based Motility in Listeria monocytogenes. Wang J, et al. Infect Immun, 2015 Sep. PMID 26169271, Free PMC Article
    4. Clinicopathological and prognostic significance of Ras association and pleckstrin homology domains 1 (RAPH1) in breast cancer. Kurozumi S, et al. Breast Cancer Res Treat, 2018 Nov. PMID 30056565
    5. Systematic identification and molecular characterization of genes differentially expressed in breast and ovarian cancer. Dahl E, et al. J Pathol, 2005 Jan. PMID 15586368

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Nuclear isoform of RAPH1 interacts with FOXQ1 to promote aggressiveness and radioresistance in breast cancer.
      Title: Nuclear isoform of RAPH1 interacts with FOXQ1 to promote aggressiveness and radioresistance in breast cancer.
    2. High RAPH1 expression is correlated with aggressive breast cancer phenotypes and provides independent prognostic value in invasive breast cancer.
      Title: Clinicopathological and prognostic significance of Ras association and pleckstrin homology domains 1 (RAPH1) in breast cancer.
    3. The human RAPH1 gene is the CHE2 locus.
      Title: Association between RAPH1 Gene Haplotypes and CHE2 Locus Phenotypes.
    4. these studies demonstrate an insight into how the Lpd-PH domain regulates cellular signals in a PI(3,4)P2 dependent manner.
      Title: Mechanistic insights into the phosphatidylinositol binding properties of the pleckstrin homology domain of lamellipodin.
    5. Disruption of the RIAM/lamellipodin-integrin-talin complex markedly impairs cell migration.
      Title: A RIAM/lamellipodin-talin-integrin complex forms the tip of sticky fingers that guide cell migration.
    6. The authors propose that Lpd delivers Ena/VASP proteins to growing barbed ends and increases their actin polymerase activity by tethering them to actin filaments.
      Title: Lamellipodin promotes actin assembly by clustering Ena/VASP proteins and tethering them to actin filaments.
    7. These data indicate a possible role for Lpd in the actin-based movement and the cell-to-cell spread of L. monocytogenes.
      Title: Lamellipodin Is Important for Cell-to-Cell Spread and Actin-Based Motility in Listeria monocytogenes.
    8. The results suggest that although the RAPH1 gene was deleted or amplified in all samples, the Lpd does not seem to play a major role in tumorigenesis of mammary carcinomas.
      Title: Amplification and deletion of the RAPH1 gene in breast cancer patients.
    9. this study suggests a novel mechanism in which Lpd mediates EGFR endocytosis via Mena downstream of endophilin.
      Title: Endophilin, Lamellipodin, and Mena cooperate to regulate F-actin-dependent EGF-receptor endocytosis.
    10. The crystal structure of Lpd cc-RA-PH presents a molecular model of Lpd enhances actin polymerization by oligomerization via two intermolecular contact sites.
      Title: Crystal structure of Lamellipodin implicates diverse functions in actin polymerization and Ras signaling.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1681

    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 axon extension IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in filopodium IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lamellipodium IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ras-associated and pleckstrin homology domains-containing protein 1
    Names
    amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18
    amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9
    lamellipodin
    proline-rich EVH1 ligand 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001329728.2 → NP_001316657.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC018891
      UniProtKB/TrEMBL
      C9J164
      Conserved Domains (3) summary
      cd01259
      Location:444 → 566
      PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
      pfam00169
      Location:449 → 557
      PH; PH domain
      cl00155
      Location:321 → 402
      UBQ; Ubiquitin-like proteins

    2. NM_203365.4 → NP_976241.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform 3

      See identical proteins and their annotated locations for NP_976241.1

      Status: REVIEWED

      Source sequence(s)
      AC018891, AI217860, AY523978, BE967038
      Consensus CDS
      CCDS2360.1
      UniProtKB/TrEMBL
      C9J164
      Related
      ENSP00000311293.4, ENST00000308091.8
      Conserved Domains (3) summary
      cd01259
      Location:444 → 566
      PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
      pfam00169
      Location:449 → 557
      PH; PH domain
      cl00155
      Location:321 → 402
      UBQ; Ubiquitin-like proteins

    3. NM_213589.3 → NP_998754.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_998754.1

      Status: REVIEWED

      Source sequence(s)
      AC018891, AI217860, AJ584699, AY494951, CA503229
      Consensus CDS
      CCDS2359.1
      UniProtKB/Swiss-Prot
      Q70E73, Q96Q37, Q9C0I2
      Related
      ENSP00000316543.5, ENST00000319170.10
      Conserved Domains (3) summary
      cd01259
      Location:392 → 514
      PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
      pfam00169
      Location:397 → 505
      PH; PH domain
      cl00155
      Location:269 → 350
      UBQ; Ubiquitin-like proteins

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      203433682..203535301 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445545.1 → XP_047301501.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

    2. XM_047445544.1 → XP_047301500.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X5

    3. XM_005246777.5 → XP_005246834.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      See identical proteins and their annotated locations for XP_005246834.1

      UniProtKB/TrEMBL
      C9K0J5
      Related
      ENSP00000486548.1, ENST00000630330.2
      Conserved Domains (3) summary
      cd01259
      Location:444 → 566
      PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
      pfam00169
      Location:449 → 557
      PH; PH domain
      cl00155
      Location:321 → 402
      UBQ; Ubiquitin-like proteins

    4. XM_047445548.1 → XP_047301504.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X8

      UniProtKB/Swiss-Prot
      Q70E73, Q96Q37, Q9C0I2

    5. XM_047445546.1 → XP_047301502.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

    6. XM_011511646.4 → XP_011509948.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      See identical proteins and their annotated locations for XP_011509948.1

      UniProtKB/TrEMBL
      C9K0J5
      Conserved Domains (3) summary
      cd01259
      Location:444 → 566
      PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
      pfam00169
      Location:449 → 557
      PH; PH domain
      cl00155
      Location:321 → 402
      UBQ; Ubiquitin-like proteins

    7. XM_047445547.1 → XP_047301503.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X7

    8. XM_047445543.1 → XP_047301499.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X4

    9. XM_047445542.1 → XP_047301498.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X3

    10. XM_047445538.1 → XP_047301494.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X1

    11. XM_047445540.1 → XP_047301496.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    12. XM_047445541.1 → XP_047301497.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    13. XM_047445539.1 → XP_047301495.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    14. XM_006712695.4 → XP_006712758.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      See identical proteins and their annotated locations for XP_006712758.1

      UniProtKB/TrEMBL
      C9K0J5
      Conserved Domains (3) summary
      cd01259
      Location:444 → 566
      PH_APBB1IP; Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain
      pfam00169
      Location:449 → 557
      PH; PH domain
      cl00155
      Location:321 → 402
      UBQ; Ubiquitin-like proteins

    15. XM_047445549.1 → XP_047301505.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X9

    16. XM_047445551.1 → XP_047301507.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X11

      Related
      ENSP00000411138.1, ENST00000439222.5

    17. XM_047445550.1 → XP_047301506.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X10

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      203915590..204017213 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343441.1 → XP_054199416.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

    2. XM_054343440.1 → XP_054199415.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X5

    3. XM_054343436.1 → XP_054199411.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    4. XM_054343443.1 → XP_054199418.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X8

      UniProtKB/Swiss-Prot
      Q70E73, Q96Q37, Q9C0I2

    5. XM_054343442.1 → XP_054199417.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X6

    6. XM_054343437.1 → XP_054199412.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    7. XM_054343439.1 → XP_054199414.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    8. XM_054343438.1 → XP_054199413.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      C9K0J5

    9. XM_054343444.1 → XP_054199419.1  ras-associated and pleckstrin homology domains-containing protein 1 isoform X9

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_051287.1: Suppressed sequence

      Description
      NG_051287.1: This RefSeq was removed by NCBI staff. Please email info@ncbi.nlm.nih.gov for more information.

    2. NM_025252.3: Suppressed sequence

      Description
      NM_025252.3: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q70E73.3 GenPept UniProtKB/Swiss-Prot:Q70E73

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