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

Gene ID: 23151, updated on 14-Nov-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
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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: 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. 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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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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