Aliases for DENND5B Gene

Aliases for DENND5B Gene

  • DENN Domain Containing 5B 2 3 5
  • DENN Domain-Containing Protein 5B 3 4
  • DENN/MADD Domain Containing 5B 2 3
  • Rab6IP1-Like Protein 3 4
  • MGC24039 2
  • DENND5B 5

External Ids for DENND5B Gene

Previous GeneCards Identifiers for DENND5B Gene

  • GC12M031426
  • GC12M031535
  • GC12M031287
  • GC12M031384
  • GC12M031385
  • GC12M031394
  • GC12M031395
  • GC12M031393
  • GC12M031392
  • GC12M031386
  • GC12M031387
  • GC12M031388
  • GC12M031389
  • GC12M031390

Summaries for DENND5B Gene

GeneCards Summary for DENND5B Gene

DENND5B (DENN Domain Containing 5B) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs. Gene Ontology (GO) annotations related to this gene include calcium channel activity and Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is DENND5A.

UniProtKB/Swiss-Prot Summary for DENND5B Gene

  • Guanine nucleotide exchange factor (GEF) which may activate RAB39A and/or RAB39B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DENND5B Gene

Genomics for DENND5B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DENND5B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J031587 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 255.3 +0.9 914 4.8 CHD2 ZBTB10 MXD4 FEZF1 FOXA1 ZNF217 BHLHE40 ZIC2 HOMEZ KDM6A DENND5B MN297144 DENND5B-AS1 DDX11 IPO8 SINHCAF AK4P3 DDX11-AS1 HSALNG0090208
GH12J031649 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 260.4 -60.8 -60835 4.2 MNT DEK IKZF1 IRF2 HES1 CTCF BHLHE40 CEBPB ARNT REST DENND5B ENSG00000287388 RNU5F-4P DENND5B-AS1 AK4P3 ETFBKMT AMN1
GH12J031495 Promoter 0.3 EPDnew 260.7 +95.2 95200 0.1 DENND5B DENND5B-AS1 RNU5F-4P ENSG00000201228 ENSG00000256159 SINHCAF
GH12J031368 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 15.4 +220.8 220801 3.7 FOXA1 IKZF1 BHLHE40 ZNF511 FOXA2 VEZF1 KLF7 ETV4 RARA TEAD3 LINC02387 DENND5B DENND5B-AS1 RNU5F-4P SINHCAF AK4P3 DDX11 ETFBKMT HSALNG0090199 lnc-SINHCAF-3
GH12J031316 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 9.8 +269.1 269081 10.8 TBP ZBTB10 BCL11A MNT IKZF1 SMAD5 IRF2 MBD2 POLR2A ZEB1 SINHCAF DDX11 IPO8 FLJ13224 RESF1 ENSG00000256984 DENND5B-AS1 DENND5B RNU5F-4P lnc-DENND5B-3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DENND5B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DENND5B

Top Transcription factor binding sites by QIAGEN in the DENND5B gene promoter:
  • HNF-1
  • HNF-1A
  • Pax-3
  • RP58

Genomic Locations for DENND5B Gene

Latest Assembly
chr12:31,382,226-31,591,136
(GRCh38/hg38)
Size:
208,911 bases
Orientation:
Minus strand

Previous Assembly
chr12:31,535,160-31,744,070
(GRCh37/hg19 by Entrez Gene)
Size:
208,911 bases
Orientation:
Minus strand

chr12:31,535,157-31,744,031
(GRCh37/hg19 by Ensembl)
Size:
208,875 bases
Orientation:
Minus strand

Genomic View for DENND5B Gene

Genes around DENND5B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DENND5B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DENND5B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DENND5B Gene

Proteins for DENND5B Gene

  • Protein details for DENND5B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZUT9-DEN5B_HUMAN
    Recommended name:
    DENN domain-containing protein 5B
    Protein Accession:
    Q6ZUT9
    Secondary Accessions:
    • B5ME75
    • Q59FW8
    • Q68CZ7
    • Q6NUJ0
    • Q7Z3F9
    • Q8N973
    • Q8WUC8

    Protein attributes for DENND5B Gene

    Size:
    1274 amino acids
    Molecular mass:
    145020 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC04583.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for DENND5B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DENND5B Gene

Post-translational modifications for DENND5B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for DENND5B Gene

Domains & Families for DENND5B Gene

Gene Families for DENND5B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for DENND5B Gene

Suggested Antigen Peptide Sequences for DENND5B Gene

GenScript: Design optimal peptide antigens:
  • Rab6IP1-like protein (DEN5B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZUT9

UniProtKB/Swiss-Prot:

DEN5B_HUMAN :
  • Belongs to the RAB6IP1 family.
Family:
  • Belongs to the RAB6IP1 family.
genes like me logo Genes that share domains with DENND5B: view

Function for DENND5B Gene

Molecular function for DENND5B Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) which may activate RAB39A and/or RAB39B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form.

Phenotypes From GWAS Catalog for DENND5B Gene

Gene Ontology (GO) - Molecular Function for DENND5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IEA,IDA 20937701
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with DENND5B: view
genes like me logo Genes that share phenotypes with DENND5B: view

miRNA for DENND5B Gene

miRTarBase miRNAs that target DENND5B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DENND5B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DENND5B Gene

Localization for DENND5B Gene

Subcellular locations from UniProtKB/Swiss-Prot for DENND5B Gene

Membrane. Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DENND5B gene
Compartment Confidence
cytosol 4
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubules (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DENND5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with DENND5B: view

Pathways & Interactions for DENND5B Gene

genes like me logo Genes that share pathways with DENND5B: view

Pathways by source for DENND5B Gene

Gene Ontology (GO) - Biological Process for DENND5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050790 regulation of catalytic activity IEA --
genes like me logo Genes that share ontologies with DENND5B: view

No data available for SIGNOR curated interactions for DENND5B Gene

Drugs & Compounds for DENND5B Gene

No Compound Related Data Available

Transcripts for DENND5B Gene

mRNA/cDNA for DENND5B Gene

6 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DENND5B

Alternative Splicing Database (ASD) splice patterns (SP) for DENND5B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - - -
SP2: - - -
SP3:
SP4:

ExUns: 22 ^ 23 ^ 24
SP1:
SP2:
SP3:
SP4:

Relevant External Links for DENND5B Gene

GeneLoc Exon Structure for
DENND5B

Expression for DENND5B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DENND5B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DENND5B Gene

This gene is overexpressed in Breast (60.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DENND5B Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DENND5B

SOURCE GeneReport for Unigene cluster for DENND5B Gene:

Hs.118166

Evidence on tissue expression from TISSUES for DENND5B Gene

  • Nervous system(4.7)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with DENND5B: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DENND5B Gene

Orthologs for DENND5B Gene

This gene was present in the common ancestor of animals.

Orthologs for DENND5B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia DENND5B 30 31
  • 99.84 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia DENND5B 31
  • 97 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia DENND5B 30 31
  • 92.75 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia DENND5B 30 31
  • 92.61 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Dennd5b 30 17 31
  • 90.66 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Dennd5b 30
  • 89.13 (n)
Oppossum
(Monodelphis domestica)
Mammalia DENND5B 31
  • 88 (a)
OneToOne
Chicken
(Gallus gallus)
Aves DENND5B 30 31
  • 80.51 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia DENND5B 31
  • 91 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia dennd5b 30
  • 74.99 (n)
Str.10985 30
Zebrafish
(Danio rerio)
Actinopterygii dennd5b 30 31
  • 68.15 (n)
OneToOne
wufb96b01 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG7852 30 31
  • 52.03 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011351 30
  • 50.78 (n)
Worm
(Caenorhabditis elegans)
Secernentea lst-6 31
  • 32 (a)
OneToMany
Species where no ortholog for DENND5B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for DENND5B Gene

ENSEMBL:
Gene Tree for DENND5B (if available)
TreeFam:
Gene Tree for DENND5B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DENND5B: view image

Paralogs for DENND5B Gene

Paralogs for DENND5B Gene

(8) SIMAP similar genes for DENND5B Gene using alignment to 4 proteins:

  • DEN5B_HUMAN
  • F5H4A0_HUMAN
  • G3V1S3_HUMAN
  • H0YGE5_HUMAN
genes like me logo Genes that share paralogs with DENND5B: view

Variants for DENND5B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DENND5B Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs1056320 - p.His487Asn
rs4930979 - p.Arg52Lys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for DENND5B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for DENND5B Gene

Variant ID Type Subtype PubMed ID
dgv2473n54 CNV loss 21841781
dgv2474n54 CNV gain+loss 21841781
dgv2475n54 CNV gain 21841781
esv2659095 CNV deletion 23128226
esv2663530 CNV deletion 23128226
esv2751046 CNV gain 17911159
esv2760267 CNV gain+loss 21179565
esv28191 CNV loss 19812545
esv3398944 CNV insertion 20981092
esv3629047 CNV loss 21293372
esv3629048 CNV gain 21293372
esv3629049 CNV loss 21293372
nsv1070522 CNV deletion 25765185
nsv52934 CNV deletion 16902084
nsv558088 CNV loss 21841781
nsv558089 CNV gain+loss 21841781
nsv558090 CNV gain+loss 21841781
nsv558092 CNV gain 21841781
nsv558099 CNV loss 21841781
nsv832364 CNV loss 17160897
nsv832365 CNV loss 17160897

Variation tolerance for DENND5B Gene

Residual Variation Intolerance Score: 8.22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.12; 96.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DENND5B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DENND5B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DENND5B Gene

Disorders for DENND5B Gene

Additional Disease Information for DENND5B

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for DENND5B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DENND5B Gene

Publications for DENND5B Gene

  1. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. (PMID: 20937701) Yoshimura S … Barr FA (The Journal of cell biology 2010) 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3
  4. Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. (PMID: 32694731) Aregger M … Moffat J (Nature metabolism 2020) 3
  5. POH1 contributes to hyperactivation of TGF-β signaling and facilitates hepatocellular carcinoma metastasis through deubiquitinating TGF-β receptors and caveolin-1. (PMID: 30745168) Wang B … Liu Y (EBioMedicine 2019) 3

Products for DENND5B Gene

  • Biorbyt antibodies for DENND5B

Sources for DENND5B Gene