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    GRAMD2B GRAM domain containing 2B [ Homo sapiens (human) ]

    Gene ID: 65983, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GRAMD2Bprovided by HGNC
    Official Full Name
    GRAM domain containing 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:24911
    See related
    Ensembl:ENSG00000155324 MIM:620182; AllianceGenome:HGNC:24911
    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
    GRAMD3; NS3TP2
    Summary
    Enables identical protein binding activity. Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 12.1), thyroid (RPKM 10.5) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GRAMD2B in Genome Data Viewer
    Location:
    5q23.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (126360120..126494364)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (126876891..127011484)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (125695812..125830056)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901056 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:125525281-125525880 Neighboring gene long intergenic non-protein coding RNA 2039 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:125564748-125564901 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:125573255-125574454 Neighboring gene uncharacterized LOC101927488 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:125695125-125696324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:125703101-125703842 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:125703843-125704583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:125706699-125707223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:125707224-125707747 Neighboring gene uncharacterized LOC101927514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16281 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:125780518-125781717 Neighboring gene NANOG hESC enhancer GRCh37_chr5:125828434-125828989 Neighboring gene Sharpr-MPRA regulatory region 10286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23023 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:125886595-125886696 Neighboring gene uncharacterized LOC124901189 Neighboring gene MPRA-validated peak5455 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:125903752-125904497 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:125933215-125933378 Neighboring gene hESC enhancers GRCh37_chr5:125935721-125936570 and GRCh37_chr5:125936571-125937418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:125937419-125938267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:125954191-125954723 Neighboring gene MPRA-validated peak5456 silencer Neighboring gene aldehyde dehydrogenase 7 family member A1 Neighboring gene phosphorylated adaptor for RNA export

    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. GRAM domain proteins specialize functionally distinct ER-PM contact sites in human cells. Besprozvannaya M, et al. Elife, 2018 Feb 22. PMID 29469807, Free PMC Article
    2. Genome-wide meta-analysis for severe diabetic retinopathy. Grassi MA, et al. Hum Mol Genet, 2011 Jun 15. PMID 21441570, Free PMC Article
    3. MTR120/KIAA1383, a novel microtubule-associated protein, promotes microtubule stability and ensures cytokinesis. Fong KW, et al. J Cell Sci, 2013 Feb 1. PMID 23264731, Free PMC Article
    4. Common genetic variation and performance on standardized cognitive tests. Cirulli ET, et al. Eur J Hum Genet, 2010 Jul. PMID 20125193, Free PMC Article
    5. The interactome of metabolic enzyme carbonic anhydrase IX reveals novel roles in tumor cell migration and invadopodia/MMP14-mediated invasion. Swayampakula M, et al. Oncogene, 2017 Nov 9. PMID 28692057, Free PMC Article

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    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

    EBI GWAS Catalog

    Description
    Common genetic variation and performance on standardized cognitive tests.
    EBI GWAS Catalog
    Genome-wide meta-analysis for severe diabetic retinopathy.
    EBI GWAS Catalog

    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

    • FLJ21313

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasmic microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic microtubule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    GRAM domain-containing protein 2B
    Names
    GRAM domain containing 3
    GRAM domain-containing protein 3
    HCV NS3-transactivated protein 2
    hepatitis C virus nonstructural protein 3-transactivating protein 2

    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_001146319.3 → NP_001139791.1  GRAM domain-containing protein 2B isoform 1

      See identical proteins and their annotated locations for NP_001139791.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC008546, AC093535, AK024966, AK300154, BC008590, CB306011, DC424558
      Consensus CDS
      CCDS54891.1
      UniProtKB/TrEMBL
      E9PD09
      Related
      ENSP00000426120.1, ENST00000513040.5
      Conserved Domains (1) summary
      cd13220
      Location:137 → 229
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    2. NM_001146320.3 → NP_001139792.1  GRAM domain-containing protein 2B isoform 3

      See identical proteins and their annotated locations for NP_001139792.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and initiates translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, AK024966, AK293307, CB306011, CF994851
      Consensus CDS
      CCDS54894.1
      UniProtKB/TrEMBL
      B7Z4W8
      Related
      ENSP00000444049.1, ENST00000544396.5
      Conserved Domains (1) summary
      cd13220
      Location:18 → 110
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    3. NM_001146321.3 → NP_001139793.1  GRAM domain-containing protein 2B isoform 4

      See identical proteins and their annotated locations for NP_001139793.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and translation initiates at an alternate start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, AK024966, AK296267, CB306011, CF994851
      Consensus CDS
      CCDS54892.1
      UniProtKB/Swiss-Prot
      Q96HH9
      Related
      ENSP00000441876.1, ENST00000542322.5
      Conserved Domains (1) summary
      cd13220
      Location:130 → 222
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    4. NM_001146322.3 → NP_001139794.1  GRAM domain-containing protein 2B isoform 5

      See identical proteins and their annotated locations for NP_001139794.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and translation initiates at an alternate start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, AK024966, AK303857, CB306011, DC413835
      Consensus CDS
      CCDS54893.1
      UniProtKB/TrEMBL
      E9PD09
      Related
      ENSP00000426088.1, ENST00000511134.1
      Conserved Domains (1) summary
      cd13220
      Location:106 → 198
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    5. NM_001349541.2 → NP_001336470.1  GRAM domain-containing protein 2B isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and initiates translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (6) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, BC008590, BP194080, CB306011, CF994851
      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:122 → 214
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    6. NM_001349542.2 → NP_001336471.1  GRAM domain-containing protein 2B isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and initiates translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (7) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, AK024966, AK303857, BC008590, BP194080, CB306011, CF994851
      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:106 → 198
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    7. NM_001349543.2 → NP_001336472.1  GRAM domain-containing protein 2B isoform 8

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and initiates translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (8) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, BC008590, BP194080, CB306011, CF994851, CN311105
      UniProtKB/TrEMBL
      B7Z4W8
      Conserved Domains (1) summary
      cd13220
      Location:18 → 110
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    8. NM_001349544.2 → NP_001336473.1  GRAM domain-containing protein 2B isoform 9

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and initiates translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (9) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, BC008590, BP194080, CB306011, CF994851, DB477009
      Related
      ENSP00000426143.1, ENST00000515200.5
      Conserved Domains (1) summary
      cd13220
      Location:130 → 222
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    9. NM_023927.4 → NP_076416.2  GRAM domain-containing protein 2B isoform 2

      See identical proteins and their annotated locations for NP_076416.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093535, AK024966, BC008590, CB306011, CF994851
      Consensus CDS
      CCDS4136.1
      UniProtKB/Swiss-Prot
      B7Z1F2, B7Z3R1, B7Z6D8, B7Z8T2, D3DSZ3, Q96HH9, Q9H753
      UniProtKB/TrEMBL
      E9PD09
      Related
      ENSP00000285689.3, ENST00000285689.8
      Conserved Domains (1) summary
      cd13220
      Location:122 → 214
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    RNA

    1. NR_146195.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC093535, AK024966, AK296267, BM729036, CB306011, CF994851, DC341655

    2. NR_146196.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC093535, AK024966, AK296267, BM729036, CB306011, CF994851

    3. NR_146197.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC093535, AK024966, AK296267, BM729036, BP194080, CB306011, CF994851, DC300218

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      126360120..126494364
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009781.2 → XP_016865270.1  GRAM domain-containing protein 2B isoform X1

      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:104 → 196
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    2. XM_011543593.3 → XP_011541895.1  GRAM domain-containing protein 2B isoform X3

      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:137 → 229
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    3. XM_047417608.1 → XP_047273564.1  GRAM domain-containing protein 2B isoform X6

    4. XM_005272057.5 → XP_005272114.1  GRAM domain-containing protein 2B isoform X4

      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:136 → 228
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    5. XM_005272058.5 → XP_005272115.1  GRAM domain-containing protein 2B isoform X5

      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:136 → 228
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    6. XM_047417610.1 → XP_047273566.1  GRAM domain-containing protein 2B isoform X8

    7. XM_047417609.1 → XP_047273565.1  GRAM domain-containing protein 2B isoform X7

    8. XM_047417611.1 → XP_047273567.1  GRAM domain-containing protein 2B isoform X9

    9. XM_047417612.1 → XP_047273568.1  GRAM domain-containing protein 2B isoform X10

    10. XM_047417613.1 → XP_047273569.1  GRAM domain-containing protein 2B isoform X1

    11. XM_047417614.1 → XP_047273570.1  GRAM domain-containing protein 2B isoform X1

    12. XM_011543594.3 → XP_011541896.1  GRAM domain-containing protein 2B isoform X9

      See identical proteins and their annotated locations for XP_011541896.1

      UniProtKB/TrEMBL
      E9PD09
      Conserved Domains (1) summary
      cd13220
      Location:106 → 198
      PH-GRAM_GRAMDC; GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    13. XM_011543591.3 → XP_011541893.2  GRAM domain-containing protein 2B isoform X1

    14. XM_011543592.4 → XP_011541894.2  GRAM domain-containing protein 2B isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      126876891..127011484
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353280.1 → XP_054209255.1  GRAM domain-containing protein 2B isoform X1

    2. XM_054353272.1 → XP_054209247.1  GRAM domain-containing protein 2B isoform X3

    3. XM_054353275.1 → XP_054209250.1  GRAM domain-containing protein 2B isoform X6

    4. XM_054353274.1 → XP_054209249.1  GRAM domain-containing protein 2B isoform X5

    5. XM_054353273.1 → XP_054209248.1  GRAM domain-containing protein 2B isoform X4

    6. XM_054353277.1 → XP_054209252.1  GRAM domain-containing protein 2B isoform X8

    7. XM_054353276.1 → XP_054209251.1  GRAM domain-containing protein 2B isoform X7

    8. XM_054353279.1 → XP_054209254.1  GRAM domain-containing protein 2B isoform X10

    9. XM_054353281.1 → XP_054209256.1  GRAM domain-containing protein 2B isoform X1

    10. XM_054353278.1 → XP_054209253.1  GRAM domain-containing protein 2B isoform X9

    11. XM_054353270.1 → XP_054209245.1  GRAM domain-containing protein 2B isoform X1

    12. XM_054353271.1 → XP_054209246.1  GRAM domain-containing protein 2B isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96HH9.1 GenPept UniProtKB/Swiss-Prot:Q96HH9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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