U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

DENND3 DENN domain containing 3 [ Homo sapiens (human) ]

Gene ID: 22898, updated on 8-Dec-2022

Summary

Official Symbol
DENND3provided by HGNC
Official Full Name
DENN domain containing 3provided by HGNC
Primary source
HGNC:HGNC:29134
See related
Ensembl:ENSG00000105339 MIM:617503; AllianceGenome:HGNC:29134
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
Summary
Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in cellular protein catabolic process; endosome to lysosome transport; and regulation of Rab protein signal transduction. Predicted to be located in cytosol. Predicted to be active in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in bone marrow (RPKM 17.0), lung (RPKM 14.2) and 23 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See DENND3 in Genome Data Viewer
Location:
8q24.3
Exon count:
31
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (141128589..141195804)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (142248713..142315919)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (142138688..142205903)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902030 Neighboring gene uncharacterized LOC105375784 Neighboring gene DENND3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 5779 Neighboring gene uncharacterized LOC105375785 Neighboring gene solute carrier family 45 member 4 Neighboring gene SLC45A4 antisense RNA 1

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?

Phenotypes

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Single-nucleotide polymorphisms in HLA- and non-HLA genes associated with the development of antibodies to interferon-β therapy in multiple sclerosis patients.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0870

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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
 
Process Evidence Code Pubs
involved_in endosome to lysosome transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of Rab protein signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
DENN domain-containing protein 3
Names
DENN/MADD domain containing 3

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001352890.3NP_001339819.2  DENN domain-containing protein 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC040970, BC110827, BX331731, CA413644
    Consensus CDS
    CCDS87629.1
    UniProtKB/TrEMBL
    E9PF32
    Related
    ENSP00000428714.1, ENST00000519811.6
    Conserved Domains (5) summary
    smart00801
    Location:435497
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:10281063
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl25539
    Location:10041276
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_001352891.3NP_001339820.2  DENN domain-containing protein 3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC040970, AL544320, BC110827, BX331731
    Related
    ENSP00000430695.1, ENST00000518347.5
    Conserved Domains (1) summary
    cl04085
    Location:122158
    uDENN; uDENN domain
  3. NM_001362798.2NP_001349727.1  DENN domain-containing protein 3 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AA760923, AC040970
    Conserved Domains (5) summary
    smart00801
    Location:435497
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:10281063
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl25539
    Location:10191120
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. NM_014957.5NP_055772.3  DENN domain-containing protein 3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC040970, BX331731, CB989310
    Consensus CDS
    CCDS34947.1
    Related
    ENSP00000262585.2, ENST00000262585.6
    Conserved Domains (5) summary
    smart00801
    Location:368430
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:961996
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:118304
    DENN; DENN (AEX-3) domain
    cl04085
    Location:5591
    uDENN; uDENN domain
    cl25539
    Location:9371209
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

  1. NR_148197.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC040970, BC110827, BX331731, CA413644

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    141128589..141195804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516933.3XP_011515235.2  DENN domain-containing protein 3 isoform X1

    Conserved Domains (5) summary
    smart00801
    Location:435497
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:10281063
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl25539
    Location:10191120
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. XM_011516934.4XP_011515236.2  DENN domain-containing protein 3 isoform X6

    Conserved Domains (5) summary
    smart00801
    Location:435497
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:10281063
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl25539
    Location:10191120
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  3. XM_047421591.1XP_047277547.1  DENN domain-containing protein 3 isoform X3

  4. XM_047421595.1XP_047277551.1  DENN domain-containing protein 3 isoform X10

  5. XM_005250841.5XP_005250898.3  DENN domain-containing protein 3 isoform X4

    Related
    ENSP00000428276.1, ENST00000518668.5
    Conserved Domains (5) summary
    smart00801
    Location:393445
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:9761011
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl25539
    Location:9521224
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  6. XM_047421592.1XP_047277548.1  DENN domain-containing protein 3 isoform X7

  7. XM_047421598.1XP_047277554.1  DENN domain-containing protein 3 isoform X13

  8. XM_047421593.1XP_047277549.1  DENN domain-containing protein 3 isoform X8

  9. XM_047421597.1XP_047277553.1  DENN domain-containing protein 3 isoform X12

  10. XM_005250840.6XP_005250897.3  DENN domain-containing protein 3 isoform X2

    Conserved Domains (5) summary
    smart00801
    Location:393445
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    sd00039
    Location:9761011
    7WD40; WD40 repeat [structural motif]
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl25539
    Location:9671068
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  11. XM_005250842.5XP_005250899.1  DENN domain-containing protein 3 isoform X5

    Conserved Domains (6) summary
    smart00801
    Location:357419
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    COG2319
    Location:9191108
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:950985
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:9411042
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    cl04085
    Location:122158
    uDENN; uDENN domain
    cl11519
    Location:170293
    DENN; DENN (AEX-3) domain
  12. XM_047421594.1XP_047277550.1  DENN domain-containing protein 3 isoform X9

  13. XM_047421596.1XP_047277552.1  DENN domain-containing protein 3 isoform X11

  14. XM_047421599.1XP_047277555.1  DENN domain-containing protein 3 isoform X14

  15. XM_011516937.3XP_011515239.2  DENN domain-containing protein 3 isoform X16

    Conserved Domains (3) summary
    smart00801
    Location:435497
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:185371
    DENN; DENN (AEX-3) domain
    cl04085
    Location:122158
    uDENN; uDENN domain
  16. XM_017013242.2XP_016868731.1  DENN domain-containing protein 3 isoform X15

    Conserved Domains (5) summary
    smart00801
    Location:187249
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    COG2319
    Location:749938
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:780815
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:771872
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    cl11519
    Location:6123
    DENN; DENN (AEX-3) domain
  17. XM_047421600.1XP_047277556.1  DENN domain-containing protein 3 isoform X18

  18. XM_011516938.4XP_011515240.1  DENN domain-containing protein 3 isoform X17

    Conserved Domains (4) summary
    smart00801
    Location:91153
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    COG2319
    Location:653842
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:684719
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:675776
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  19. XM_047421601.1XP_047277557.1  DENN domain-containing protein 3 isoform X20

  20. XM_011516939.4XP_011515241.1  DENN domain-containing protein 3 isoform X19

    See identical proteins and their annotated locations for XP_011515241.1

    Conserved Domains (3) summary
    COG2319
    Location:496685
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:527562
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:518619
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  21. XM_011516940.3XP_011515242.1  DENN domain-containing protein 3 isoform X19

    See identical proteins and their annotated locations for XP_011515242.1

    Conserved Domains (3) summary
    COG2319
    Location:496685
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:527562
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:518619
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

  1. XR_007060719.1 RNA Sequence

  2. XR_007060720.1 RNA Sequence

  3. XR_928312.4 RNA Sequence

  4. XR_007060722.1 RNA Sequence

  5. XR_007060721.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    142248713..142315919
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)