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    RAPGEFL1 Rap guanine nucleotide exchange factor like 1 [ Homo sapiens (human) ]

    Gene ID: 51195, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RAPGEFL1provided by HGNC
    Official Full Name
    Rap guanine nucleotide exchange factor like 1provided by HGNC
    Primary source
    HGNC:HGNC:17428
    See related
    Ensembl:ENSG00000108352 AllianceGenome:HGNC:17428
    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
    Link-GEFII
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in Ras protein signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in skin (RPKM 52.1), esophagus (RPKM 22.9) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAPGEFL1 in Genome Data Viewer
    Location:
    17q21.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (40177010..40195650)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (41040889..41059520)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38333263..38351902)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8480 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:38279065-38279703 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38296401-38297341 Neighboring gene MSL complex subunit 1 Neighboring gene CASC3 exon junction complex subunit Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38324317-38324876 Neighboring gene microRNA 6866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38332602-38333102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38333103-38333603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38333995-38334850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38334851-38335705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38350695-38351195 Neighboring gene microRNA 6867 Neighboring gene Sharpr-MPRA regulatory region 10842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:38375397-38376175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38380779-38381350 Neighboring gene WAS/WASL interacting protein family member 2 Neighboring gene RNY4 pseudogene 8 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:38437298-38438234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:38438235-38439169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38443891-38444698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38447656-38448242 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:38452145-38452660 Neighboring gene cell division cycle 6

    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. Screening aberrant methylation profile in esophageal squamous cell carcinoma for Kazakhs in Xinjiang area of China. Chen Y, et al. Mol Biol Rep, 2015 Feb. PMID 25304811
    2. Estimation of the fraction of cancer cells in a tumor DNA sample using DNA methylation. Takahashi T, et al. PLoS One, 2013. PMID 24312652, Free PMC Article
    3. Identification of guanine nucleotide exchange factors (GEFs) for the Rap1 GTPase. Regulation of MR-GEF by M-Ras-GTP interaction. Rebhun JF, et al. J Biol Chem, 2000 Nov 10. PMID 10934204
    4. Cytoskeletal scaffolding proteins interact with Lynch-Syndrome associated mismatch repair protein MLH1. Brieger A, et al. Proteomics, 2010 Sep. PMID 20706999
    5. N(6)-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cheng Y, et al. Cancer Cell, 2021 Jul 12. PMID 34048709, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    • MGC134798, MGC134799

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		  
    involved_in Ras protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    rap guanine nucleotide exchange factor-like 1
    Names
    Link guanine nucleotide exchange factor II
    Rap guanine nucleotide exchange factor (GEF)-like 1
    link GEFII

    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.

    Genomic

    1. NG_054939.1 RefSeqGene

      Range
      5461..23641
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001303533.2 → NP_001290462.1  rap guanine nucleotide exchange factor-like 1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (1) is shorter at the N-terminus compared to isoform 3.
      Source sequence(s)
      AC068669, AK313492, BU620139, DB265550
      Consensus CDS
      CCDS77022.1
      UniProtKB/TrEMBL
      B7Z8Y5
      Related
      ENSP00000394530.2, ENST00000456989.6

    2. NM_001303534.3 → NP_001290463.1  rap guanine nucleotide exchange factor-like 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 3.
      Source sequence(s)
      AC068669, AK304160, BU620139
      Consensus CDS
      CCDS77023.1
      UniProtKB/TrEMBL
      B7Z8Y5, F5H2D5
      Related
      ENSP00000438631.1, ENST00000544503.5
      Conserved Domains (1) summary
      smart00147
      Location:263 → 501
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases

    3. NM_016339.6 → NP_057423.2  rap guanine nucleotide exchange factor-like 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) encodes the longest isoform (3).
      Source sequence(s)
      AC068669, BC029956, BC115375, BU620139
      Consensus CDS
      CCDS11363.2
      UniProtKB/Swiss-Prot
      Q9UHV5
      UniProtKB/TrEMBL
      A0A087WVW6
      Related
      ENSP00000479735.1, ENST00000620260.6
      Conserved Domains (1) summary
      smart00147
      Location:420 → 658
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      40177010..40195650
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436203.1 → XP_047292159.1  rap guanine nucleotide exchange factor-like 1 isoform X1

      UniProtKB/TrEMBL
      A0A087WVW6

    2. XM_047436205.1 → XP_047292161.1  rap guanine nucleotide exchange factor-like 1 isoform X4

      Related
      ENSP00000264644.5, ENST00000264644.10

    3. XM_047436204.1 → XP_047292160.1  rap guanine nucleotide exchange factor-like 1 isoform X2

    4. XM_006721938.4 → XP_006722001.1  rap guanine nucleotide exchange factor-like 1 isoform X3

      See identical proteins and their annotated locations for XP_006722001.1

      UniProtKB/TrEMBL
      B4DGK9
      Conserved Domains (1) summary
      smart00147
      Location:150 → 388
      RasGEF; Guanine nucleotide exchange factor for Ras-like small GTPases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      41040889..41059520
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316355.1 → XP_054172330.1  rap guanine nucleotide exchange factor-like 1 isoform X1

      UniProtKB/TrEMBL
      A0A087WVW6

    2. XM_054316358.1 → XP_054172333.1  rap guanine nucleotide exchange factor-like 1 isoform X4

    3. XM_054316356.1 → XP_054172331.1  rap guanine nucleotide exchange factor-like 1 isoform X2

    4. XM_054316357.1 → XP_054172332.1  rap guanine nucleotide exchange factor-like 1 isoform X3

      UniProtKB/TrEMBL
      B4DGK9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHV5.2 GenPept UniProtKB/Swiss-Prot:Q9UHV5

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