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DENND2B DENN domain containing 2B [ Homo sapiens (human) ]

Gene ID: 6764, updated on 2-Nov-2024

Summary

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Official Symbol
DENND2Bprovided by HGNC
Official Full Name
DENN domain containing 2Bprovided by HGNC
Primary source
HGNC:HGNC:11350
See related
Ensembl:ENSG00000166444 MIM:140750; AllianceGenome:HGNC:11350
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
ST5; HTS1; p126
Summary
This gene was identified by its ability to suppress the tumorigenicity of Hela cells in nude mice. The protein encoded by this gene contains a C-terminal region that shares similarity with the Rab 3 family of small GTP binding proteins. This protein preferentially binds to the SH3 domain of c-Abl kinase, and acts as a regulator of MAPK1/ERK2 kinase, which may contribute to its ability to reduce the tumorigenic phenotype in cells. Three alternatively spliced transcript variants of this gene encoding distinct isoforms are identified. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in endometrium (RPKM 30.7), testis (RPKM 16.0) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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See DENND2B in Genome Data Viewer
Location:
11p15.4
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (8693352..8910951, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (8775106..8995121, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (8714899..8932498, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4390 Neighboring gene Sharpr-MPRA regulatory region 3983 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8719729-8720516 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8720517-8721302 Neighboring gene small nucleolar RNA, H/ACA box 3A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8723665-8724450 Neighboring gene small nucleolar RNA, H/ACA box 3B Neighboring gene ribosomal protein L27a Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:8731697-8732198 Neighboring gene uncharacterized LOC107984308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8780393-8780893 Neighboring gene DENND2B antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8827143-8827644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8827645-8828144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:8850107-8850606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8853387-8854188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8854189-8854989 Neighboring gene RNA, 5S ribosomal pseudogene 330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8884480-8884980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8884981-8885481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4395 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8946857-8947641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8947642-8948425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8954113-8954951 Neighboring gene chromosome 11 open reading frame 16 Neighboring gene A-kinase interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4397 Neighboring gene achaete-scute family bHLH transcription factor 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DENND2B activates Rab35 at the intercellular bridge, regulating cytokinetic abscission and tetraploidy.
    Title: DENND2B activates Rab35 at the intercellular bridge, regulating cytokinetic abscission and tetraploidy.
  2. Findings provide evidence of suppression of tumorigenicity 5 (ST5) involvement in positive regulation of osteoclastogenesis via src Kinases (Src)/Syk Kinase (Syk)/calcium signaling.
    Title: ST5 Positively Regulates Osteoclastogenesis via Src/Syk/calcium Signaling Pathways.
  3. Here, we discover that intersectin-s binds DENND2B, a guanine nucleotide exchange factor for the exocytic GTPase Rab13, and this interaction promotes recycling of ligand-free EGFR to the cell surface. Our study thus reveals a novel mechanism controlling the fate of internalized EGFR with important implications for cancer.
    Title: Intersectin-s interaction with DENND2B facilitates recycling of epidermal growth factor receptor.
  4. DENND2B interacts with the Rab13 effector MICAL-L2 at the cell periphery, and this interaction is required for the dynamic remodeling of the cell's leading edge.
    Title: DENND2B activates Rab13 at the leading edge of migrating cells and promotes metastatic behavior.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  6. Using RNA in situ hybridisation in mouse, the authors found that St5 is expressed in the frontal cortex during embryonic development. In adult mouse brain, expression of St5 was especially high in the hippocampal area and cerebellum.
    Title: Disruption of ST5 is associated with mental retardation and multiple congenital anomalies.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC33090

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within positive regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cell cortex IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in recycling endosome IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
DENN domain-containing protein 2B
Names
DENN/MADD domain containing 2B
heLa tumor suppression 1
suppression of tumorigenicity 5 protein

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_029450.1 RefSeqGene

    Range
    105278..222600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001376495.1 → NP_001363424.1  DENN domain-containing protein 2B isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7791.1
    UniProtKB/Swiss-Prot
    B2R6X7, B3KXQ6, P78523, P78524, Q16492, Q7KYY2, Q7KZ12, Q8NE12, Q9BQQ6
    Conserved Domains (4) summary
    smart00801
    Location:1023 → 1089
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:697 → 784
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    PHA03247
    Location:46 → 411
    PHA03247; large tegument protein UL36; Provisional
    pfam02141
    Location:791 → 972
    DENN; DENN (AEX-3) domain

  2. NM_001376496.1 → NP_001363425.1  DENN domain-containing protein 2B isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7791.1
    UniProtKB/Swiss-Prot
    B2R6X7, B3KXQ6, P78523, P78524, Q16492, Q7KYY2, Q7KZ12, Q8NE12, Q9BQQ6
    Conserved Domains (4) summary
    smart00801
    Location:1023 → 1089
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:697 → 784
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    PHA03247
    Location:46 → 411
    PHA03247; large tegument protein UL36; Provisional
    pfam02141
    Location:791 → 972
    DENN; DENN (AEX-3) domain

  3. NM_001376497.1 → NP_001363426.1  DENN domain-containing protein 2B isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7791.1
    UniProtKB/Swiss-Prot
    B2R6X7, B3KXQ6, P78523, P78524, Q16492, Q7KYY2, Q7KZ12, Q8NE12, Q9BQQ6
    Conserved Domains (4) summary
    smart00801
    Location:1023 → 1089
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:697 → 784
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    PHA03247
    Location:46 → 411
    PHA03247; large tegument protein UL36; Provisional
    pfam02141
    Location:791 → 972
    DENN; DENN (AEX-3) domain

  4. NM_001376498.1 → NP_001363427.1  DENN domain-containing protein 2B isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Conserved Domains (3) summary
    smart00801
    Location:854 → 920
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    PHA03247
    Location:46 → 411
    PHA03247; large tegument protein UL36; Provisional
    pfam02141
    Location:622 → 803
    DENN; DENN (AEX-3) domain

  5. NM_001376499.1 → NP_001363428.1  DENN domain-containing protein 2B isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Conserved Domains (3) summary
    smart00801
    Location:843 → 909
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:517 → 604
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:611 → 792
    DENN; DENN (AEX-3) domain

  6. NM_001376500.1 → NP_001363429.1  DENN domain-containing protein 2B isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Conserved Domains (3) summary
    smart00801
    Location:796 → 862
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:470 → 557
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:564 → 745
    DENN; DENN (AEX-3) domain

  7. NM_001376501.1 → NP_001363430.1  DENN domain-containing protein 2B isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7792.1
    UniProtKB/TrEMBL
    B4DDL8
    Related
    ENSP00000436802.1, ENST00000530438.5
    Conserved Domains (3) summary
    smart00801
    Location:603 → 669
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:277 → 364
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:371 → 552
    DENN; DENN (AEX-3) domain

  8. NM_001376502.1 → NP_001363431.1  DENN domain-containing protein 2B isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7792.1
    UniProtKB/TrEMBL
    B4DDL8
    Conserved Domains (3) summary
    smart00801
    Location:603 → 669
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:277 → 364
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:371 → 552
    DENN; DENN (AEX-3) domain

  9. NM_001376503.1 → NP_001363432.1  DENN domain-containing protein 2B isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    UniProtKB/TrEMBL
    B4DDL8
    Conserved Domains (3) summary
    smart00801
    Location:543 → 609
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:311 → 492
    DENN; DENN (AEX-3) domain
    cl04085
    Location:277 → 314
    uDENN; uDENN domain

  10. NM_001376504.1 → NP_001363433.1  DENN domain-containing protein 2B isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    UniProtKB/TrEMBL
    B4DDL8
    Conserved Domains (3) summary
    smart00801
    Location:531 → 597
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:205 → 292
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:299 → 480
    DENN; DENN (AEX-3) domain

  11. NM_001376505.1 → NP_001363434.1  DENN domain-containing protein 2B isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS91434.1
    UniProtKB/TrEMBL
    B4DDL8
    Related
    ENSP00000432887.1, ENST00000530991.5
    Conserved Domains (3) summary
    smart00801
    Location:495 → 561
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:169 → 256
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:263 → 444
    DENN; DENN (AEX-3) domain

  12. NM_001376506.1 → NP_001363435.1  DENN domain-containing protein 2B isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS91434.1
    UniProtKB/TrEMBL
    B4DDL8
    Conserved Domains (3) summary
    smart00801
    Location:495 → 561
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:169 → 256
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:263 → 444
    DENN; DENN (AEX-3) domain

  13. NM_005418.4 → NP_005409.3  DENN domain-containing protein 2B isoform 1

    See identical proteins and their annotated locations for NP_005409.3

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7791.1
    UniProtKB/Swiss-Prot
    B2R6X7, B3KXQ6, P78523, P78524, Q16492, Q7KYY2, Q7KZ12, Q8NE12, Q9BQQ6
    Related
    ENSP00000433528.1, ENST00000534127.5
    Conserved Domains (4) summary
    smart00801
    Location:1023 → 1089
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:697 → 784
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    PHA03247
    Location:46 → 411
    PHA03247; large tegument protein UL36; Provisional
    pfam02141
    Location:791 → 972
    DENN; DENN (AEX-3) domain

  14. NM_139157.3 → NP_631896.1  DENN domain-containing protein 2B isoform 2

    See identical proteins and their annotated locations for NP_631896.1

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053
    Consensus CDS
    CCDS7792.1
    UniProtKB/TrEMBL
    B4DDL8
    Conserved Domains (3) summary
    smart00801
    Location:603 → 669
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:277 → 364
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:371 → 552
    DENN; DENN (AEX-3) domain

  15. NM_213618.2 → NP_998783.1  DENN domain-containing protein 2B isoform 1

    See identical proteins and their annotated locations for NP_998783.1

    Status: REVIEWED

    Source sequence(s)
    BC036655, BX647431, U15131, U15780
    Consensus CDS
    CCDS7791.1
    UniProtKB/Swiss-Prot
    B2R6X7, B3KXQ6, P78523, P78524, Q16492, Q7KYY2, Q7KZ12, Q8NE12, Q9BQQ6
    Related
    ENSP00000319678.6, ENST00000313726.11
    Conserved Domains (4) summary
    smart00801
    Location:1023 → 1089
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:697 → 784
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    PHA03247
    Location:46 → 411
    PHA03247; large tegument protein UL36; Provisional
    pfam02141
    Location:791 → 972
    DENN; DENN (AEX-3) domain

RNA

  1. NR_164814.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  2. NR_164815.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  3. NR_164816.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  4. NR_164817.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  5. NR_164818.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  6. NR_164819.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  7. NR_164820.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  8. NR_164821.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

  9. NR_164822.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026894, AC091053

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    8693352..8910951 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    8775106..8995121 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P78524.3 GenPept UniProtKB/Swiss-Prot:P78524

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