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DENND4C DENN domain containing 4C [ Homo sapiens (human) ]

Gene ID: 55667, updated on 5-Apr-2020

Summary

Official Symbol
DENND4Cprovided by HGNC
Official Full Name
DENN domain containing 4Cprovided by HGNC
Primary source
HGNC:HGNC:26079
See related
Ensembl:ENSG00000137145
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
C9orf55; C9orf55B; RAB10GEF; bA513M16.3
Expression
Ubiquitous expression in duodenum (RPKM 11.5), skin (RPKM 11.0) and 25 other tissues See more
Orthologs

Genomic context

See DENND4C in Genome Data Viewer
Location:
9p22.1
Exon count:
35
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (19230693..19374281)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (19230763..19374137)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr9.246 Neighboring gene ribosomal protein S6 pseudogene 10 Neighboring gene NADH:ubiquinone oxidoreductase subunit A5 pseudogene 3 Neighboring gene ribosomal protein S6

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20686, DKFZp686I09113

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cellular response to insulin stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
insulin-responsive compartment ISS
Inferred from Sequence or Structural Similarity
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
retromer complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
DENN domain-containing protein 4C
Names
DENN/MADD domain containing 4A pseudogene
DENN/MADD domain containing 4C

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_001330640.2NP_001317569.1  DENN domain-containing protein 4C isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL161909, AL391834
    Consensus CDS
    CCDS83349.1
    UniProtKB/Swiss-Prot
    Q5VZ89
    Related
    ENSP00000473469.1, ENST00000434457.6
    Conserved Domains (4) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:192276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:820849
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:309492
    DENN; DENN (AEX-3) domain
  2. NM_017925.7NP_060395.5  DENN domain-containing protein 4C isoform 1

    See identical proteins and their annotated locations for NP_060395.5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the full length protein. The exon combination is inferred and is supported by a series of overlapping partial transcripts. The annotated protein is supported by homology.
    Source sequence(s)
    AK125842, AL161909, AL391834, AW271839, CN427691, DA517991, DV080472, HY106197
    Consensus CDS
    CCDS6491.3
    UniProtKB/Swiss-Prot
    Q5VZ89
    Related
    ENSP00000473565.1, ENST00000602925.5
    Conserved Domains (4) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:192276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:820849
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:310492
    DENN; DENN (AEX-3) domain

RNA

  1. NR_073201.4 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate exons, and includes two alternate exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL161909, AL391834, AW271839, BC144485, DA517991, DV080472, HY106197

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    19230693..19374281
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014918.1XP_016870407.1  DENN domain-containing protein 4C isoform X3

    Conserved Domains (4) summary
    smart00801
    Location:323396
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:584613
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:73256
    DENN; DENN (AEX-3) domain
    cl04085
    Location:140
    uDENN; uDENN domain
  2. XM_017014919.1XP_016870408.1  DENN domain-containing protein 4C isoform X3

    Conserved Domains (4) summary
    smart00801
    Location:323396
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:584613
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:73256
    DENN; DENN (AEX-3) domain
    cl04085
    Location:140
    uDENN; uDENN domain
  3. XM_017014917.1XP_016870406.1  DENN domain-containing protein 4C isoform X2

  4. XM_017014920.1XP_016870409.1  DENN domain-containing protein 4C isoform X6

  5. XM_006716805.3XP_006716868.1  DENN domain-containing protein 4C isoform X1

    Conserved Domains (4) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:192276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:820849
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:309492
    DENN; DENN (AEX-3) domain
  6. XM_011517959.3XP_011516261.1  DENN domain-containing protein 4C isoform X4

    Conserved Domains (5) summary
    smart00801
    Location:559632
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:192276
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:820849
    PPR; PPR repeat [structural motif]
    pfam02141
    Location:309492
    DENN; DENN (AEX-3) domain
    pfam13041
    Location:819858
    PPR_2; PPR repeat family
  7. XM_006716807.4XP_006716870.1  DENN domain-containing protein 4C isoform X5

    Conserved Domains (3) summary
    smart00801
    Location:57130
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00004
    Location:318347
    PPR; PPR repeat [structural motif]
    pfam13041
    Location:317356
    PPR_2; PPR repeat family

RNA

  1. XR_001746350.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_023879.1: Suppressed sequence

    Description
    NG_023879.1: This RefSeq was suppressed because review of this locus determined that it is not a non-transcribed pseudogene; it represents a region of the DENND4C (GeneID: 55667) gene.
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