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    SH3GLB2 SH3 domain containing GRB2 like, endophilin B2 [ Homo sapiens (human) ]

    Gene ID: 56904, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SH3GLB2provided by HGNC
    Official Full Name
    SH3 domain containing GRB2 like, endophilin B2provided by HGNC
    Primary source
    HGNC:HGNC:10834
    See related
    Ensembl:ENSG00000148341 MIM:609288; AllianceGenome:HGNC:10834
    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
    RRIG1; PP6569; PP9455
    Summary
    Enables identical protein binding activity. Predicted to be involved in membrane organization and postsynaptic neurotransmitter receptor internalization. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in skin (RPKM 45.1), prostate (RPKM 29.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SH3GLB2 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129007036..129028331, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141210470..141231788, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131769315..131790610, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131708642-131709204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131709205-131709766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:131709767-131710328 Neighboring gene nucleoporin 188 Neighboring gene dolichol kinase Neighboring gene uncharacterized LOC101929314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131773679-131774589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131784821-131785628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131785629-131786436 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:131788471-131789034 and GRCh37_chr9:131789035-131789598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131789599-131790162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131790847-131791586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131791587-131792326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29101 Neighboring gene mitoguardin 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:131821359-131822558 Neighboring gene uncharacterized LOC124902334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29102 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131833123-131834072 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131834073-131835022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20359 Neighboring gene dolichyldiphosphatase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Tumor-suppressor activity of RRIG1 in breast cancer. Zhang G, et al. BMC Cancer, 2011 Jan 25. PMID 21266059, Free PMC Article
    2. Endophilin B2 facilitates endosome maturation in response to growth factor stimulation, autophagy induction, and influenza A virus infection. Serfass JM, et al. J Biol Chem, 2017 Jun 16. PMID 28455444, Free PMC Article
    3. Endophilin B2 promotes inner mitochondrial membrane degradation by forming heterodimers with Endophilin B1 during mitophagy. Wang YH, et al. Sci Rep, 2016 Apr 26. PMID 27112121, Free PMC Article
    4. The Bin/amphiphysin/Rvs (BAR) domain protein endophilin B2 interacts with plectin and controls perinuclear cytoskeletal architecture. Vannier C, et al. J Biol Chem, 2013 Sep 20. PMID 23921385, Free PMC Article
    5. SPAS-1 (stimulator of prostatic adenocarcinoma-specific T cells)/SH3GLB2: A prostate tumor antigen identified by CTLA-4 blockade. Fassò M, et al. Proc Natl Acad Sci U S A, 2008 Mar 4. PMID 18303116, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Here the authors report that Endophilin B2, similarly to Endophilin B1, plays an indispensable role in mitochondria sequestration and inner mitochondrial membrane (IMM) protein degradation during mitophagy.
      Title: Endophilin B2 promotes inner mitochondrial membrane degradation by forming heterodimers with Endophilin B1 during mitophagy.
    2. Data (including data from studies in knockout mice) suggest that SH3GLB2 regulates trafficking of endocytic vesicles and autophagosomes to late endosomes or lysosomes; despite having an intracellular localization and tissue distribution similar to endophilin B1, endophilin B2 is dispensable for mitochondrial apoptosis.
      Title: Endophilin B2 facilitates endosome maturation in response to growth factor stimulation, autophagy induction, and influenza A virus infection.
    3. the potential importance of the endophilin B2-plectin complex in the biological functions depending on nuclear migration and positioning.
      Title: The Bin/amphiphysin/Rvs (BAR) domain protein endophilin B2 interacts with plectin and controls perinuclear cytoskeletal architecture.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. identified a nonmutated HLA-A2-binding epitope in the human ortholog SH3GLB2, which primed T cells from healthy HLA-A2(+) individuals
      Title: SPAS-1 (stimulator of prostatic adenocarcinoma-specific T cells)/SH3GLB2: A prostate tumor antigen identified by CTLA-4 blockade.
    Submit: New GeneRIF Correction

    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1848

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in membrane organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    endophilin-B2
    Names
    SH3 domain-containing GRB2-like protein B2
    SH3-containing protein SH3GLB2
    SH3-domain GRB2-like endophilin B2
    retinoid receptor-induced gene 1

    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_001287045.2 → NP_001273974.1  endophilin-B2 isoform a

      See identical proteins and their annotated locations for NP_001273974.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AB058751, AL592211, BC005843, BM808895
      Consensus CDS
      CCDS69680.1
      UniProtKB/Swiss-Prot
      Q9NR46
      Related
      ENSP00000361634.4, ENST00000372554.8
      Conserved Domains (2) summary
      cd07617
      Location:21 → 282
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:348 → 402
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    2. NM_001287046.2 → NP_001273975.1  endophilin-B2 isoform b

      See identical proteins and their annotated locations for NP_001273975.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons in the central coding region, and also lacks a segment of the 3' UTR, compared to variant 1. The encoded isoform (b) is shorter than isoform a. Both variants 2 and 3 encode isoform b.
      Source sequence(s)
      AF257319, BC005843, BM808895
      Consensus CDS
      CCDS6916.1
      UniProtKB/Swiss-Prot
      A6NC47, A8MPS4, Q8WY61, Q96JH9, Q9NR46
      Related
      ENSP00000361640.1, ENST00000372559.5
      Conserved Domains (2) summary
      cd07617
      Location:21 → 278
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:339 → 393
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    3. NM_001369913.1 → NP_001356842.1  endophilin-B2 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (c).
      Source sequence(s)
      AL592211
      Conserved Domains (2) summary
      cd07617
      Location:32 → 293
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:359 → 413
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    4. NM_001369914.1 → NP_001356843.1  endophilin-B2 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL592211
      Conserved Domains (1) summary
      cd07617
      Location:21 → 282
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2

    5. NM_001369915.1 → NP_001356844.1  endophilin-B2 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL592211
      Conserved Domains (2) summary
      cd07617
      Location:21 → 257
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:323 → 377
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    6. NM_020145.4 → NP_064530.1  endophilin-B2 isoform b

      See identical proteins and their annotated locations for NP_064530.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a. Both variants 2 and 3 encode isoform b.
      Source sequence(s)
      AB058751, AL592211, BC005843, BC014635, BM808895
      Consensus CDS
      CCDS6916.1
      UniProtKB/Swiss-Prot
      A6NC47, A8MPS4, Q8WY61, Q96JH9, Q9NR46
      Related
      ENSP00000361645.3, ENST00000372564.8
      Conserved Domains (2) summary
      cd07617
      Location:21 → 278
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:339 → 393
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    RNA

    1. NR_163192.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL592211

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      129007036..129028331 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005252101.4 → XP_005252158.1  endophilin-B2 isoform X8

      See identical proteins and their annotated locations for XP_005252158.1

      UniProtKB/Swiss-Prot
      Q9NR46
      Conserved Domains (1) summary
      cl17036
      Location:65 → 125
      SH3; Src Homology 3 domain superfamily

    2. XM_047423606.1 → XP_047279562.1  endophilin-B2 isoform X7

      UniProtKB/TrEMBL
      B7ZC39
      Related
      ENSP00000388282.1, ENST00000416629.5

    3. XM_005252098.3 → XP_005252155.1  endophilin-B2 isoform X5

      See identical proteins and their annotated locations for XP_005252155.1

      UniProtKB/TrEMBL
      B7ZC38
      Related
      ENSP00000402566.1, ENST00000417224.5
      Conserved Domains (2) summary
      cd07617
      Location:21 → 278
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:344 → 398
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    4. XM_047423605.1 → XP_047279561.1  endophilin-B2 isoform X4

    5. XM_006717189.3 → XP_006717252.1  endophilin-B2 isoform X2

      Conserved Domains (2) summary
      cd07617
      Location:21 → 302
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:368 → 422
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    6. XM_006717191.2 → XP_006717254.1  endophilin-B2 isoform X6

      See identical proteins and their annotated locations for XP_006717254.1

      Conserved Domains (2) summary
      cd07617
      Location:21 → 282
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:343 → 397
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    7. XM_006717190.2 → XP_006717253.1  endophilin-B2 isoform X3

      Conserved Domains (2) summary
      cd07617
      Location:21 → 306
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:367 → 421
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    8. XM_006717188.3 → XP_006717251.1  endophilin-B2 isoform X1

      Conserved Domains (2) summary
      cd07617
      Location:21 → 306
      BAR_Endophilin_B2; The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2
      cd11944
      Location:372 → 426
      SH3_Endophilin_B2; Src homology 3 domain of Endophilin-B2

    9. XM_047423607.1 → XP_047279563.1  endophilin-B2 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      141210470..141231788 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363313.1 → XP_054219288.1  endophilin-B2 isoform X8

    2. XM_054363312.1 → XP_054219287.1  endophilin-B2 isoform X7

      UniProtKB/TrEMBL
      B7ZC39

    3. XM_054363310.1 → XP_054219285.1  endophilin-B2 isoform X5

      UniProtKB/TrEMBL
      B7ZC38

    4. XM_054363309.1 → XP_054219284.1  endophilin-B2 isoform X4

    5. XM_054363307.1 → XP_054219282.1  endophilin-B2 isoform X2

    6. XM_054363311.1 → XP_054219286.1  endophilin-B2 isoform X6

    7. XM_054363308.1 → XP_054219283.1  endophilin-B2 isoform X3

    8. XM_054363306.1 → XP_054219281.1  endophilin-B2 isoform X1

    9. XM_054363314.1 → XP_054219289.1  endophilin-B2 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NR46.1 GenPept UniProtKB/Swiss-Prot:Q9NR46

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