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

Gene ID: 10260, updated on 3-Nov-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
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Genomic context

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See DENND4A in Genome Data Viewer
Location:
15q22.31
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (65659123..65792293, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (63468521..63601729, complement)
RS_2024_09 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 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 (46) 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_2024_08

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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