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

Gene ID: 65983, updated on 3-Apr-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, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 12.1), thyroid (RPKM 10.5) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
5q23.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (126360120..126494364)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (126876891..127011484)
105.20220307 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
  • 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_2023_10

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

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