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    SRGAP2B SLIT-ROBO Rho GTPase activating protein 2B [ Homo sapiens (human) ]

    Gene ID: 647135, updated on 17-Jun-2024

    Summary

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    Official Symbol
    SRGAP2Bprovided by HGNC
    Official Full Name
    SLIT-ROBO Rho GTPase activating protein 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:35237
    See related
    Ensembl:ENSG00000196369 MIM:614703; AllianceGenome:HGNC:35237
    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
    SRGAP2L; SRGAP2P2
    Summary
    This locus encodes a member of the SLIT-ROBO Rho GTPase activating protein family. This human-specific locus resulted from incomplete segmental duplication of the SLIT-ROBO Rho GTPase activating protein 2 locus. The encoded protein lacks the GTPase activating protein domain compared to proteins encoded by SLIT-ROBO Rho GTPase activating protein 2. The functionality of the protein encoded by this locus has been questioned, as several normal individuals with homozygous deletions for this locus have been identified, and the expression of this locus appears to be much lower than the similar SLIT-ROBO Rho GTPase activating protein 2C (SRGAP2C) locus. The SRGAP2C locus has been shown to encode a protein that functions antagonistically to SLIT-ROBO Rho GTPase activating protein 2 in cortical neuron development. [provided by RefSeq, Dec 2012]
    Expression
    Ubiquitous expression in skin (RPKM 9.5), spleen (RPKM 7.9) and 23 other tissues See more
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    Genomic context

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    See SRGAP2B in Genome Data Viewer
    Location:
    1q21.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (144887288..145095380, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (144012035..144220090, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (206100298..206137837, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724269 Neighboring gene immunoglobulin kappa variable 1-39-like Neighboring gene uncharacterized LOC107985595 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:144076705-144077206 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144028101-144028601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144017621-144018286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:144011847-144012347 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144010333-144011311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144009352-144010332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:144008259-144008767 Neighboring gene Sharpr-MPRA regulatory region 15698 duplicate 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:144006805-144007304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:143989479-143990347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:143986871-143987740 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:143944389-143945152 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:143938883-143939875 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:143934844-143935344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:143913587-143914089 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:143912345-143912912 Neighboring gene family with sequence similarity 72 member D Neighboring gene Sharpr-MPRA regulatory region 11936 Neighboring gene tRNA-Asn (anticodon GTT) 10-1 Neighboring gene myomegalin-like

    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
    • 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. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Dennis MY, et al. Cell, 2012 May 11. PMID 22559943, Free PMC Article
    2. Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Charrier C, et al. Cell, 2012 May 11. PMID 22559944, Free PMC Article
    3. Transcriptional fates of human-specific segmental duplications in brain. Dougherty ML, et al. Genome Res, 2018 Oct. PMID 30228200, Free PMC Article
    4. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Choy KW, et al. Physiol Genomics, 2006 Mar 13. PMID 16368877
    5. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Dias Neto E, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10737800, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    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

    • WI2-929E21

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SLIT-ROBO Rho GTPase-activating protein 2B
    Names
    SLIT-ROBO Rho GTPase activating protein 2 pseudogene 2
    SLIT-ROBO Rho GTPase activating protein 2B (pseudogene)

    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_001271870.5 → NP_001258799.2  SLIT-ROBO Rho GTPase-activating protein 2B isoform 1

      See identical proteins and their annotated locations for NP_001258799.2

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      Consensus CDS
      CCDS72854.2
      UniProtKB/TrEMBL
      A0A286YEY3
      Related
      ENSP00000493121.1, ENST00000641863.3
      Conserved Domains (1) summary
      cl12013
      Location:26 → 289
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. NM_001330684.2 → NP_001317613.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      UniProtKB/TrEMBL
      E9PDX4
      Conserved Domains (1) summary
      cl12013
      Location:1 → 135
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    3. NM_001366280.2 → NP_001353209.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      Consensus CDS
      CCDS91032.1
      UniProtKB/Swiss-Prot
      P0DMP2
      Related
      ENSP00000477776.1, ENST00000612199.4
      Conserved Domains (1) summary
      cl12013
      Location:26 → 288
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    4. NM_001368324.2 → NP_001355253.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      UniProtKB/TrEMBL
      E9PDX4

    5. NM_001385226.1 → NP_001372155.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      Conserved Domains (1) summary
      cl12013
      Location:26 → 319
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    6. NM_001385227.1 → NP_001372156.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      Conserved Domains (1) summary
      cl12013
      Location:26 → 268
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    7. NM_001385228.1 → NP_001372157.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC242498, FP700111
      UniProtKB/TrEMBL
      E9PDX4
      Conserved Domains (1) summary
      cl12013
      Location:52 → 199
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      144887288..145095380 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005277421.5 → XP_005277478.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X2

      See identical proteins and their annotated locations for XP_005277478.1

      UniProtKB/TrEMBL
      E9PDX4
      Conserved Domains (1) summary
      cl12013
      Location:1 → 136
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. XM_047428007.1 → XP_047283963.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X2

      UniProtKB/TrEMBL
      E9PDX4

    3. XM_047428008.1 → XP_047283964.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X3

      UniProtKB/TrEMBL
      E9PDX4

    4. XM_005277422.5 → XP_005277479.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X2

      See identical proteins and their annotated locations for XP_005277479.1

      UniProtKB/TrEMBL
      E9PDX4
      Conserved Domains (1) summary
      cl12013
      Location:1 → 136
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    5. XM_017002087.3 → XP_016857576.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X1

      Conserved Domains (1) summary
      cl12013
      Location:26 → 277
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      144012035..144220090 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338263.1 → XP_054194238.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X3

      UniProtKB/TrEMBL
      E9PDX4

    2. XM_054338260.1 → XP_054194235.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X2

      UniProtKB/TrEMBL
      E9PDX4

    3. XM_054338259.1 → XP_054194234.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X2

      UniProtKB/TrEMBL
      E9PDX4

    4. XM_054338262.1 → XP_054194237.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X3

      UniProtKB/TrEMBL
      E9PDX4

    5. XM_054338261.1 → XP_054194236.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X2

      UniProtKB/TrEMBL
      E9PDX4

    6. XM_054338258.1 → XP_054194233.1  SLIT-ROBO Rho GTPase-activating protein 2B isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_012336.1: Suppressed sequence

      Description
      NG_012336.1: This RefSeq was permanently suppressed because it is now thought that this pseudogene is transcribed.

    2. NR_034178.1: Suppressed sequence

      Description
      NR_034178.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DMP2.1 GenPept UniProtKB/Swiss-Prot:P0DMP2

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