Format

Send to:

Choose Destination

DENND1B DENN domain containing 1B [ Homo sapiens (human) ]

Gene ID: 163486, updated on 1-Aug-2020

Summary

Official Symbol
DENND1Bprovided by HGNC
Official Full Name
DENN domain containing 1Bprovided by HGNC
Primary source
HGNC:HGNC:28404
See related
Ensembl:ENSG00000213047 MIM:613292
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
FAM31B; C1ORF18; C1orf218
Summary
Clathrin (see MIM 118955)-mediated endocytosis is a major mechanism for internalization of proteins and lipids. Members of the connecdenn family, such as DENND1B, function as guanine nucleotide exchange factors (GEFs) for the early endosomal small GTPase RAB35 (MIM 604199) and bind to clathrin and clathrin adaptor protein-2 (AP2; see MIM 601024). Thus, connecdenns link RAB35 activation with the clathrin machinery (Marat and McPherson, 2010 [PubMed 20154091]).[supplied by OMIM, Nov 2010]
Expression
Ubiquitous expression in colon (RPKM 1.5), thyroid (RPKM 1.4) and 25 other tissues See more
Orthologs

Genomic context

See DENND1B in Genome Data Viewer
Location:
1q31.3
Exon count:
30
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (197504748..197782138, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (197473878..197744623, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATPase H+ transporting accessory protein 2 pseudogene Neighboring gene crumbs cell polarity complex component 1 Neighboring gene mitochondrial ribosomal protein S21 pseudogene 3 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 32 Neighboring gene RPL24 pseudogene 5 Neighboring gene family with sequence similarity 204 member B, pseudogene Neighboring gene chromosome 1 open reading frame 53 Neighboring gene LIM homeobox 9

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

NHGRI GWAS Catalog

Description
Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling.
NHGRI GWA Catalog
Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Variants of DENND1B associated with asthma in children.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20054, FLJ21179, FLJ33888, MGC27044, MGC103810, DKFZp547O0715

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rab guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Rab guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
T cell receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
T cell receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
T-helper 2 cell cytokine production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
T-helper 2 cell cytokine production IMP
Inferred from Mutant Phenotype
more info
PubMed 
endocytic recycling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endocytic recycling ISS
Inferred from Sequence or Structural Similarity
more info
 
endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
protein transport IEA
Inferred from Electronic Annotation
more info
 
regulation of immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
clathrin-coated vesicle IEA
Inferred from Electronic Annotation
more info
 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear speck IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
DENN domain-containing protein 1B
Names
DENN/MADD domain containing 1B
connecdenn 2
family with sequence similarity 31, member B

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_001195215.2NP_001182144.1  DENN domain-containing protein 1B isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AI692985, AK093982, AL139136, BC074735, BK006960, BP220095, DA495773
    Consensus CDS
    CCDS72997.1
    UniProtKB/Swiss-Prot
    Q6P3S1
    Related
    ENSP00000479816.1, ENST00000620048.6
    Conserved Domains (3) summary
    smart00801
    Location:323388
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:94291
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:989
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  2. NM_001195216.2NP_001182145.1  DENN domain-containing protein 1B isoform 4

    See identical proteins and their annotated locations for NP_001182145.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 3. The resulting isoform (4) has a distinct C-terminus and is shorter than isoform 3.
    Source sequence(s)
    BC063456, DA495773
    UniProtKB/Swiss-Prot
    Q6P3S1
    Related
    ENST00000468589.5
  3. NM_001300858.2NP_001287787.1  DENN domain-containing protein 1B isoform 5

    See identical proteins and their annotated locations for NP_001287787.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains multiple differences at the 5' and 3' ends, compared to variant 3, including initiation of translation at an alternate start codon. The resulting isoform (5) has distinct N- and C-termini and is shorter than isoform 3.
    Source sequence(s)
    AL139136, BC022561, BC063877, DA495773
    Consensus CDS
    CCDS72996.1
    UniProtKB/Swiss-Prot
    Q6P3S1
    Related
    ENSP00000235453.4, ENST00000235453.8
    Conserved Domains (3) summary
    smart00801
    Location:293358
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:84261
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:1179
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  4. NM_144977.5NP_659414.2  DENN domain-containing protein 1B isoform 2

    See identical proteins and their annotated locations for NP_659414.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 3. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 3.
    Source sequence(s)
    AL139136, BC063877, DA495773
    Consensus CDS
    CCDS41452.2
    UniProtKB/Swiss-Prot
    Q6P3S1
    Related
    ENSP00000356366.3, ENST00000367396.7
    Conserved Domains (3) summary
    smart00801
    Location:323388
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:94291
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:989
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

RNA

  1. NR_125340.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks three alternate internal exons, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 3, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI692985, AK091207, AK093982, AL139136, BC074735, BK006960, DA495773

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    197504748..197782138 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509248.2XP_011507550.1  DENN domain-containing protein 1B isoform X3

    Conserved Domains (3) summary
    smart00801
    Location:336401
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:107304
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:22102
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  2. XM_006711193.3XP_006711256.1  DENN domain-containing protein 1B isoform X4

    See identical proteins and their annotated locations for XP_006711256.1

    Conserved Domains (3) summary
    smart00801
    Location:313378
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:84281
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:1179
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  3. XM_017000470.1XP_016855959.1  DENN domain-containing protein 1B isoform X4

    Conserved Domains (3) summary
    smart00801
    Location:313378
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:84281
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:1179
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  4. XM_005244931.2XP_005244988.1  DENN domain-containing protein 1B isoform X5

    See identical proteins and their annotated locations for XP_005244988.1

    Conserved Domains (3) summary
    smart00801
    Location:303368
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:94271
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:989
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  5. XM_024453627.1XP_024309395.1  DENN domain-containing protein 1B isoform X8

    Conserved Domains (1) summary
    smart00801
    Location:39104
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
  6. XM_017000471.1XP_016855960.1  DENN domain-containing protein 1B isoform X6

    UniProtKB/TrEMBL
    A0A024R987
    Conserved Domains (3) summary
    smart00801
    Location:293358
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:84261
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:1179
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  7. XM_006711192.2XP_006711255.1  DENN domain-containing protein 1B isoform X4

    See identical proteins and their annotated locations for XP_006711255.1

    Conserved Domains (3) summary
    smart00801
    Location:313378
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:84281
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:1179
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  8. XM_024453626.1XP_024309394.1  DENN domain-containing protein 1B isoform X7

    Conserved Domains (2) summary
    smart00801
    Location:122187
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:190
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
  9. XM_011509249.2XP_011507551.1  DENN domain-containing protein 1B isoform X4

    See identical proteins and their annotated locations for XP_011507551.1

    Conserved Domains (3) summary
    smart00801
    Location:313378
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:84281
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:1179
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  10. XM_011509247.1XP_011507549.1  DENN domain-containing protein 1B isoform X2

    Conserved Domains (3) summary
    smart00801
    Location:351416
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:142319
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:57137
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  11. XM_011509246.2XP_011507548.1  DENN domain-containing protein 1B isoform X1

    Conserved Domains (3) summary
    smart00801
    Location:371436
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:142339
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:57137
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
  12. XM_006711194.3XP_006711257.1  DENN domain-containing protein 1B isoform X9

    Conserved Domains (1) summary
    smart00801
    Location:1782
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
  13. XM_011509251.3XP_011507553.1  DENN domain-containing protein 1B isoform X10

    Conserved Domains (3) summary
    smart00801
    Location:371434
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:142339
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:57137
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001142795.1: Suppressed sequence

    Description
    NM_001142795.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  2. NM_019049.1: Suppressed sequence

    Description
    NM_019049.1: This RefSeq was suppressed because the CDS was partial.
Support Center