Format

Send to:

Choose Destination

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

Gene ID: 10260, updated on 7-Jul-2019

Summary

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
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

Genomic context

See DENND4A in Genome Data Viewer
Location:
15q22.31
Exon count:
34
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (65655234..65792293, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (65952954..66084631, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene integrator complex subunit 14 Neighboring gene uncharacterized LOC102723464 Neighboring gene solute carrier family 24 member 1 Neighboring gene small nucleolar RNA, C/D box 13E Neighboring gene microRNA 4511 Neighboring gene DnaJ heat shock protein family (Hsp40) member B14 pseudogene Neighboring gene uncharacterized LOC105370866 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 44 Neighboring gene tRNA-Gln (anticodon CTG) 1-4

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystem (from REACTOME)
    RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystemHuman cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of d...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33949, KIAA0476

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
Rab guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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_001144823.2NP_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
    Consensus CDS
    CCDS53949.1
    UniProtKB/Swiss-Prot
    Q7Z401
    UniProtKB/TrEMBL
    Q05C90
    Related
    ENSP00000391167.3, ENST00000443035.7
    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  2. NM_001320835.1NP_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
    Related
    ENSP00000489304.1, ENST00000635620.1
    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  3. NM_005848.4NP_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
    Q7Z401
    Related
    ENSP00000396830.2, ENST00000431932.6
    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    65655234..65792293 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005254121.4XP_005254178.1  C-myc promoter-binding protein isoform X2

    See identical proteins and their annotated locations for XP_005254178.1

    UniProtKB/Swiss-Prot
    Q7Z401
    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  2. XM_017021863.2XP_016877352.1  C-myc promoter-binding protein isoform X2

    UniProtKB/Swiss-Prot
    Q7Z401
    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  3. XM_005254120.5XP_005254177.1  C-myc promoter-binding protein isoform X1

    See identical proteins and their annotated locations for XP_005254177.1

    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  4. XM_017021865.2XP_016877354.1  C-myc promoter-binding protein isoform X8

  5. XM_024449819.1XP_024305587.1  C-myc promoter-binding protein isoform X7

    Conserved Domains (2) summary
    sd00004
    Location:76105
    PPR; PPR repeat [structural motif]
    cl25449
    Location:74114
    PPR_2; PPR repeat family
  6. XM_005254122.5XP_005254179.1  C-myc promoter-binding protein isoform X6

    Conserved Domains (2) summary
    sd00004
    Location:76105
    PPR; PPR repeat [structural motif]
    pfam13041
    Location:74114
    PPR_2; PPR repeat family
  7. XM_006720371.4XP_006720434.1  C-myc promoter-binding protein isoform X1

    See identical proteins and their annotated locations for XP_006720434.1

    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  8. XM_017021862.2XP_016877351.1  C-myc promoter-binding protein isoform X1

    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family
  9. XM_011521157.3XP_011519459.1  C-myc promoter-binding protein isoform X5

    Conserved Domains (3) summary
    smart00801
    Location:43116
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:294323
    PPR; PPR repeat [structural motif]
    pfam13041
    Location:292332
    PPR_2; PPR repeat family
  10. XM_017021864.2XP_016877353.1  C-myc promoter-binding protein isoform X3

  11. XM_011521156.3XP_011519458.1  C-myc promoter-binding protein isoform X4

    Conserved Domains (6) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:194276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:810839
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:308492
    DENN; DENN (AEX-3) domain
    pfam10240
    Location:44199
    DUF2464; Protein of unknown function (DUF2464)
    pfam13041
    Location:808848
    PPR_2; PPR repeat family

RNA

  1. XR_001751047.2 RNA Sequence

  2. XR_002957625.1 RNA Sequence

Support Center