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    DENND4A DENN domain containing 4A [ Homo sapiens (human) ]

    Gene ID: 10260, updated on 5-Mar-2024

    Summary

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    Official Symbol
    DENND4Aprovided by HGNC
    Official Full Name
    DENN domain containing 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:24321
    See related
    Ensembl:ENSG00000174485 MIM:600382; AllianceGenome:HGNC:24321
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IRLB; MYCPBP
    Summary
    This gene encodes a DENN domain-containing protein that may function as a guanine nucleotide exchange factor that specifically activates ras-related protein Rab-10. This protein also contains a interferon stimulated response element-binding domain and may be involved in regulating the v-myc avian myelocytomatosis viral (MYC) oncogene. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in bone marrow (RPKM 7.2), lymph node (RPKM 6.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q22.31
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (65659123..65792293, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (63468521..63601729, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (65951461..66084631, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr15:65871212-65871790 Neighboring gene integrator complex subunit 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9602 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:65910767-65911352 Neighboring gene uncharacterized LOC102723464 Neighboring gene solute carrier family 24 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6557 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:65943238-65943423 Neighboring gene small nucleolar RNA, C/D box 13E Neighboring gene microRNA 4511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6558 Neighboring gene DnaJ heat shock protein family (Hsp40) member B14 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6559 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:66084519-66085484 Neighboring gene uncharacterized LOC105370866 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:66102167-66102331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9606 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 44 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:66124684-66125414 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:66126147-66126877 Neighboring gene uncharacterized LOC124903586

    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. Cloning of a cDNA encoding a human protein which binds a sequence in the c-myc gene similar to the interferon-stimulated response element. Stasiv YZ, et al. Gene, 1994 Aug 5. PMID 8056341
    2. TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease. Neelagandan N, et al. Nucleic Acids Res, 2019 Jan 10. PMID 30357366, Free PMC Article
    3. Molecular cloning, structural analysis, and expression of a human IRLB, MYC promoter-binding protein: new DENN domain-containing protein family emerges. Semova N, et al. Genomics, 2003 Sep. PMID 12906859
    4. p73 Interacts with c-Myc to regulate Y-box-binding protein-1 expression. Uramoto H, et al. J Biol Chem, 2002 Aug 30. PMID 12080043
    5. The CARM1-p300-c-Myc-Max (CPCM) transcriptional complex regulates the expression of CUL4A/4B and affects the stability of CRL4 E3 ligases in colorectal cancer. Lu W, et al. Int J Biol Sci, 2020. PMID 32140074, Free PMC Article

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    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

    • FLJ33949, KIAA0476

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of Rab protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    C-myc promoter-binding protein
    Names
    DENN domain-containing protein 4A
    DENN/MADD domain containing 4A
    c-myc promoter binding 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_001144823.2 → NP_001138295.1  C-myc promoter-binding protein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform (1).
      Source sequence(s)
      AC011939, AK307411, AL833317, BC028057, BC041706
      UniProtKB/Swiss-Prot
      Q7Z401
      UniProtKB/TrEMBL
      Q05C90
      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    2. NM_001320835.1 → NP_001307764.1  C-myc promoter-binding protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      AC011939
      Consensus CDS
      CCDS92025.1
      UniProtKB/TrEMBL
      A0A7I2RAZ6
      Related
      ENSP00000391167.4, ENST00000443035.8
      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    3. NM_001376919.1 → NP_001363848.1  C-myc promoter-binding protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC011939
      Consensus CDS
      CCDS45285.1
      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93
      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Multivesicular body subunit 12
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    4. NM_001376920.1 → NP_001363849.1  C-myc promoter-binding protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC011939
      Consensus CDS
      CCDS45285.1
      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93
      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Multivesicular body subunit 12
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    5. NM_005848.4 → NP_005839.3  C-myc promoter-binding protein isoform 2

      See identical proteins and their annotated locations for NP_005839.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AC011939, BC041706, DB462436
      Consensus CDS
      CCDS45285.1
      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93
      Related
      ENSP00000396830.2, ENST00000431932.6
      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Multivesicular body subunit 12
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      65659123..65792293 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432100.1 → XP_047288056.1  C-myc promoter-binding protein isoform X5

    2. XM_047432097.1 → XP_047288053.1  C-myc promoter-binding protein isoform X4

    3. XM_047432091.1 → XP_047288047.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    4. XM_005254120.6 → XP_005254177.1  C-myc promoter-binding protein isoform X3

      See identical proteins and their annotated locations for XP_005254177.1

      UniProtKB/TrEMBL
      A0A7I2RAZ6
      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    5. XM_047432087.1 → XP_047288043.1  C-myc promoter-binding protein isoform X1

    6. XM_047432098.1 → XP_047288054.1  C-myc promoter-binding protein isoform X5

    7. XM_047432090.1 → XP_047288046.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    8. XM_047432086.1 → XP_047288042.1  C-myc promoter-binding protein isoform X1

    9. XM_047432103.1 → XP_047288059.1  C-myc promoter-binding protein isoform X6

      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93

    10. XM_047432101.1 → XP_047288057.1  C-myc promoter-binding protein isoform X5

    11. XM_047432096.1 → XP_047288052.1  C-myc promoter-binding protein isoform X4

    12. XM_047432093.1 → XP_047288049.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    13. XM_047432094.1 → XP_047288050.1  C-myc promoter-binding protein isoform X3

      UniProtKB/TrEMBL
      A0A7I2RAZ6

    14. XM_047432089.1 → XP_047288045.1  C-myc promoter-binding protein isoform X1

    15. XM_047432102.1 → XP_047288058.1  C-myc promoter-binding protein isoform X6

      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93

    16. XM_047432099.1 → XP_047288055.1  C-myc promoter-binding protein isoform X5

    17. XM_047432095.1 → XP_047288051.1  C-myc promoter-binding protein isoform X4

    18. XM_047432092.1 → XP_047288048.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27
      Related
      ENSP00000489304.2, ENST00000635620.2

    19. XM_047432088.1 → XP_047288044.1  C-myc promoter-binding protein isoform X1

    20. XM_047432104.1 → XP_047288060.1  C-myc promoter-binding protein isoform X6

      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93

    21. XM_047432105.1 → XP_047288061.1  C-myc promoter-binding protein isoform X7

    22. XM_047432106.1 → XP_047288062.1  C-myc promoter-binding protein isoform X9

    23. XM_011521156.4 → XP_011519458.1  C-myc promoter-binding protein isoform X8

      Conserved Domains (6) summary
      smart00801
      Location:559 → 632
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:194 → 276
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:810 → 839
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:308 → 492
      DENN; DENN (AEX-3) domain
      pfam10240
      Location:44 → 199
      DUF2464; Protein of unknown function (DUF2464)
      pfam13041
      Location:808 → 848
      PPR_2; PPR repeat family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      63468521..63601729 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377193.1 → XP_054233168.1  C-myc promoter-binding protein isoform X5

    2. XM_054377191.1 → XP_054233166.1  C-myc promoter-binding protein isoform X5

    3. XM_054377189.1 → XP_054233164.1  C-myc promoter-binding protein isoform X4

    4. XM_054377182.1 → XP_054233157.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    5. XM_054377185.1 → XP_054233160.1  C-myc promoter-binding protein isoform X3

      UniProtKB/TrEMBL
      A0A7I2RAZ6

    6. XM_054377178.1 → XP_054233153.1  C-myc promoter-binding protein isoform X1

    7. XM_054377190.1 → XP_054233165.1  C-myc promoter-binding protein isoform X5

    8. XM_054377181.1 → XP_054233156.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    9. XM_054377177.1 → XP_054233152.1  C-myc promoter-binding protein isoform X1

    10. XM_054377195.1 → XP_054233170.1  C-myc promoter-binding protein isoform X6

      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93

    11. XM_054377192.1 → XP_054233167.1  C-myc promoter-binding protein isoform X5

    12. XM_054377188.1 → XP_054233163.1  C-myc promoter-binding protein isoform X4

    13. XM_054377184.1 → XP_054233159.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    14. XM_054377186.1 → XP_054233161.1  C-myc promoter-binding protein isoform X3

      UniProtKB/TrEMBL
      A0A7I2RAZ6

    15. XM_054377180.1 → XP_054233155.1  C-myc promoter-binding protein isoform X1

    16. XM_054377194.1 → XP_054233169.1  C-myc promoter-binding protein isoform X6

      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93

    17. XM_054377187.1 → XP_054233162.1  C-myc promoter-binding protein isoform X4

    18. XM_054377179.1 → XP_054233154.1  C-myc promoter-binding protein isoform X1

    19. XM_054377183.1 → XP_054233158.1  C-myc promoter-binding protein isoform X2

      UniProtKB/TrEMBL
      A0A0U1RR27

    20. XM_054377196.1 → XP_054233171.1  C-myc promoter-binding protein isoform X6

      UniProtKB/Swiss-Prot
      E7EPL3, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93

    21. XM_054377197.1 → XP_054233172.1  C-myc promoter-binding protein isoform X7

    22. XM_054377198.1 → XP_054233173.1  C-myc promoter-binding protein isoform X8

    23. XM_054377199.1 → XP_054233174.1  C-myc promoter-binding protein isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z401.2 GenPept UniProtKB/Swiss-Prot:Q7Z401

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