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    GRAMD4 GRAM domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 23151, updated on 10-Dec-2024

    Summary

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    Official Symbol
    GRAMD4provided by HGNC
    Official Full Name
    GRAM domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:29113
    See related
    Ensembl:ENSG00000075240 MIM:613691; AllianceGenome:HGNC:29113
    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
    DIP
    Summary
    GRAMD4 is a mitochondrial effector of E2F1 (MIM 189971)-induced apoptosis (Stanelle et al., 2005 [PubMed 15565177]).[supplied by OMIM, Jan 2011]
    Expression
    Ubiquitous expression in colon (RPKM 10.9), small intestine (RPKM 9.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GRAMD4 in Genome Data Viewer
    Location:
    22q13.31
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (46575744..46682756)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (47062971..47170713)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (46972985..47078653)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1924 Neighboring gene uncharacterized LOC105373075 Neighboring gene long intergenic non-protein coding RNA 2925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46947509-46948008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46947007-46947508 Neighboring gene Sharpr-MPRA regulatory region 3871 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46957479-46958230 Neighboring gene Sharpr-MPRA regulatory region 8687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19242 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:46979179-46980168 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:46980169-46981156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46982145-46983132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46994829-46995328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47014315-47015082 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:47017511-47018022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:47023179-47023964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47026702-47027202 Neighboring gene Sharpr-MPRA regulatory region 10248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47057755-47058338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47065520-47066020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47079427-47079928 Neighboring gene Sharpr-MPRA regulatory region 6253 Neighboring gene ceramide kinase Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:47106581-47107780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47118736-47119253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47121804-47122304 Neighboring gene uncharacterized LOC105373077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47131961-47132534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:47134630-47135288 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:47150047-47150223 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:47157594-47158428 Neighboring gene TBC1D22A divergent transcript

    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. Gene expression changes in response to E2F1 activation. Stanelle J, et al. Nucleic Acids Res, 2002 Apr 15. PMID 11937641, Free PMC Article
    2. [Expression and clinicopathological significance of GRAMD4 in hepatocellular carcinoma]. Zhang J, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2013 Feb. PMID 23388340
    3. GRAMD4 mimics p53 and mediates the apoptotic function of p73 at mitochondria. John K, et al. Cell Death Differ, 2011 May. PMID 21127500, Free PMC Article
    4. A novel mitochondrial protein DIP mediates E2F1-induced apoptosis independently of p53. Stanelle J, et al. Cell Death Differ, 2005 Apr. PMID 15565177
    5. The Rb-related p130 protein controls telomere lengthening through an interaction with a Rad50-interacting protein, RINT-1. Kong LJ, et al. Mol Cell, 2006 Apr 7. PMID 16600870

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The expression of GRAMD4 is up-regulated in hepatocellular carcinoma cell(HCC cell) lines and HCC tissues, and the increased expression is correlated with the clinicopathological characteristics of HCC.
      Title: [Expression and clinicopathological significance of GRAMD4 in hepatocellular carcinoma].
    2. GRAMD4 induces changes in Bcl-2 and Bax protein levels
      Title: GRAMD4 mimics p53 and mediates the apoptotic function of p73 at mitochondria.
    3. 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.
    4. localizes to the mitochondria, upregulated following E2F1 induction
      Title: A novel mitochondrial protein DIP mediates E2F1-induced apoptosis independently of p53.
    5. DIP induces p53-independent caspase-dependent and -independent apoptosis. DIP is localized in the mitochondria. DIP accumulates upon E2F1 activation.
      Title: A novel mitochondrial protein DIP mediates E2F1-induced apoptosis independently of p53.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0767, MGC90497, MGC149847

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of toll-like receptor 9 signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of toll-like receptor 9 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cysteine-type endopeptidase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrial membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    GRAM domain-containing protein 4
    Names
    death-inducing-protein

    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_001366660.1 → NP_001353589.1  GRAM domain-containing protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL021392, AL096766
      Conserved Domains (3) summary
      cl17171
      Location:486 → 547
      PH-like; Pleckstrin homology-like domain
      cl25545
      Location:122 → 177
      V-ATPase_G_2; Vacuolar (H+)-ATPase G subunit
      cl25548
      Location:66 → 186
      DUF4670; Domain of unknown function (DUF4670)

    2. NM_015124.5 → NP_055939.1  GRAM domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_055939.1

      Status: VALIDATED

      Source sequence(s)
      AL021392, AL096766
      Consensus CDS
      CCDS33672.1
      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9
      Related
      ENSP00000385689.1, ENST00000406902.6
      Conserved Domains (3) summary
      cd13221
      Location:460 → 565
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam08372
      Location:305 → 397
      PRT_C; Plant phosphoribosyltransferase C-terminal
      pfam15233
      Location:73 → 142
      SYCE1; Synaptonemal complex central element protein 1

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      46575744..46682756
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006724169.2 → XP_006724232.1  GRAM domain-containing protein 4 isoform X3

      Conserved Domains (2) summary
      cd13221
      Location:483 → 588
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam15233
      Location:96 → 165
      SYCE1; Synaptonemal complex central element protein 1

    2. XM_047441210.1 → XP_047297166.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    3. XM_011530012.2 → XP_011528314.1  GRAM domain-containing protein 4 isoform X7

      Conserved Domains (3) summary
      pfam08372
      Location:305 → 397
      PRT_C; Plant phosphoribosyltransferase C-terminal
      pfam15233
      Location:73 → 142
      SYCE1; Synaptonemal complex central element protein 1
      cl17171
      Location:460 → 542
      PH-like; Pleckstrin homology-like domain

    4. XM_047441208.1 → XP_047297164.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    5. XM_011530011.2 → XP_011528313.1  GRAM domain-containing protein 4 isoform X6

      Conserved Domains (3) summary
      cd13221
      Location:460 → 545
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam08372
      Location:305 → 397
      PRT_C; Plant phosphoribosyltransferase C-terminal
      pfam15233
      Location:73 → 142
      SYCE1; Synaptonemal complex central element protein 1

    6. XM_005261396.4 → XP_005261453.1  GRAM domain-containing protein 4 isoform X2

      Conserved Domains (2) summary
      PRK09510
      Location:122 → 177
      tolA; cell envelope integrity inner membrane protein TolA; Provisional
      cd13221
      Location:486 → 591
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain

    7. XM_047441206.1 → XP_047297162.1  GRAM domain-containing protein 4 isoform X4

    8. XM_047441211.1 → XP_047297167.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    9. XM_047441209.1 → XP_047297165.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9
      Related
      ENSP00000354313.3, ENST00000361034.7

    10. XM_047441207.1 → XP_047297163.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    11. XM_047441205.1 → XP_047297161.1  GRAM domain-containing protein 4 isoform X1

    12. XM_006724170.5 → XP_006724233.1  GRAM domain-containing protein 4 isoform X5

      See identical proteins and their annotated locations for XP_006724233.1

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9
      Conserved Domains (3) summary
      cd13221
      Location:460 → 565
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam08372
      Location:305 → 397
      PRT_C; Plant phosphoribosyltransferase C-terminal
      pfam15233
      Location:73 → 142
      SYCE1; Synaptonemal complex central element protein 1

    13. XM_017028670.3 → XP_016884159.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9
      Conserved Domains (3) summary
      cd13221
      Location:460 → 565
      PH-GRAM_GRAMDC4; GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam08372
      Location:305 → 397
      PRT_C; Plant phosphoribosyltransferase C-terminal
      pfam15233
      Location:73 → 142
      SYCE1; Synaptonemal complex central element protein 1

    14. XM_011530014.2 → XP_011528316.1  GRAM domain-containing protein 4 isoform X8

      Conserved Domains (1) summary
      pfam15233
      Location:73 → 142
      SYCE1; Synaptonemal complex central element protein 1

    15. XM_047441212.1 → XP_047297168.1  GRAM domain-containing protein 4 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      47062971..47170713
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325286.1 → XP_054181261.1  GRAM domain-containing protein 4 isoform X3

    2. XM_054325293.1 → XP_054181268.1  GRAM domain-containing protein 4 isoform X7

    3. XM_054325290.1 → XP_054181265.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    4. XM_054325292.1 → XP_054181267.1  GRAM domain-containing protein 4 isoform X6

    5. XM_054325285.1 → XP_054181260.1  GRAM domain-containing protein 4 isoform X2

    6. XM_054325287.1 → XP_054181262.1  GRAM domain-containing protein 4 isoform X4

    7. XM_054325291.1 → XP_054181266.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    8. XM_054325289.1 → XP_054181264.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    9. XM_054325284.1 → XP_054181259.1  GRAM domain-containing protein 4 isoform X1

    10. XM_054325288.1 → XP_054181263.1  GRAM domain-containing protein 4 isoform X5

      UniProtKB/Swiss-Prot
      A9IN51, A9IN57, Q68EN0, Q6IC98, Q9UGE6, Q9Y4B9

    11. XM_054325294.1 → XP_054181269.1  GRAM domain-containing protein 4 isoform X8

    12. XM_054325295.1 → XP_054181270.1  GRAM domain-containing protein 4 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6IC98.1 GenPept UniProtKB/Swiss-Prot:Q6IC98

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