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    Dennd1b DENN domain containing 1B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289051, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Dennd1bprovided by RGD
    Official Full Name
    DENN domain containing 1Bprovided by RGD
    Primary source
    RGD:1308441
    See related
    EnsemblRapid:ENSRNOG00000011063 AllianceGenome:RGD:1308441
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Fam31b
    Summary
    Predicted to enable guanyl-nucleotide exchange factor activity; phosphatidylinositol phosphate binding activity; and small GTPase binding activity. Predicted to be involved in several processes, including endocytic recycling; positive regulation of GTPase activity; and positive regulation of immune response. Predicted to be located in cytoplasmic vesicle. Predicted to be active in cytosol and nuclear speck. Orthologous to human DENND1B (DENN domain containing 1B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 210.8), Heart (RPKM 124.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dennd1b in Genome Data Viewer
    Location:
    13q13
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (53096717..53324372)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (50545324..50772922)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (56015813..56242041)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481501 Neighboring gene similar to human chromosome 1 open reading frame 53 Neighboring gene uncharacterized LOC120096262 Neighboring gene uncharacterized LOC120096263 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase-like Neighboring gene crumbs cell polarity complex component 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Regulation of T Cell Receptor Signaling by DENND1B in TH2 Cells and Allergic Disease. Yang CW, et al. Cell, 2016 Jan 14. PMID 26774822
    2. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. Yoshimura S, et al. J Cell Biol, 2010 Oct 18. PMID 20937701, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables small GTPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in T cell receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of GTPase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of T-helper 2 cell cytokine production ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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

    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.

    mRNA and Protein(s)

    1. NM_001430770.1 → NP_001417699.1  DENN domain-containing protein 1B isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A8I6AN53, F1M3B0

    2. NM_001430771.1 → NP_001417700.1  DENN domain-containing protein 1B isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A8I6AN53

    3. NM_001430772.1 → NP_001417701.1  DENN domain-containing protein 1B isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A8I6AN53

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      53096717..53324372
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063272684.1 → XP_063128754.1  DENN domain-containing protein 1B isoform X5

      UniProtKB/TrEMBL
      A0A8I6G654

    2. XM_039091333.2 → XP_038947261.1  DENN domain-containing protein 1B isoform X6

      UniProtKB/TrEMBL
      A0A8I6AN53
      Conserved Domains (2) summary
      smart00801
      Location:248 → 313
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:19 → 216
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

    3. XM_003751245.4 → XP_003751293.1  DENN domain-containing protein 1B isoform X3

      Related
      ENSRNOP00000037059.6, ENSRNOT00000035129.7
      Conserved Domains (3) summary
      smart00801
      Location:323 → 388
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:94 → 291
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:9 → 89
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

    4. XM_003751244.4 → XP_003751292.1  DENN domain-containing protein 1B isoform X4

      Related
      ENSRNOP00000043081.7, ENSRNOT00000043907.8
      Conserved Domains (3) summary
      smart00801
      Location:303 → 368
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:94 → 271
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:9 → 89
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

    5. XM_008769580.3 → XP_008767802.1  DENN domain-containing protein 1B isoform X5

      See identical proteins and their annotated locations for XP_008767802.1

      UniProtKB/TrEMBL
      A0A8I6G654
      Related
      ENSRNOP00000080096.1, ENSRNOT00000094144.2
      Conserved Domains (2) summary
      smart00801
      Location:245 → 310
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:20 → 213
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

    6. XM_063272683.1 → XP_063128753.1  DENN domain-containing protein 1B isoform X2

      UniProtKB/TrEMBL
      A0A8I6AN53, D3Z8F6
      Related
      ENSRNOP00000099618.1, ENSRNOT00000136226.1

    7. XM_063272682.1 → XP_063128752.1  DENN domain-containing protein 1B isoform X1

      Related
      ENSRNOP00000082359.2, ENSRNOT00000112392.2

    8. XM_063272685.1 → XP_063128755.1  DENN domain-containing protein 1B isoform X5

      UniProtKB/TrEMBL
      A0A8I6G654

    9. XM_039091335.2 → XP_038947263.1  DENN domain-containing protein 1B isoform X7

      Conserved Domains (2) summary
      smart00801
      Location:248 → 313
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:19 → 216
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

    10. XM_039091336.1 → XP_038947264.1  DENN domain-containing protein 1B isoform X8

      Conserved Domains (2) summary
      smart00801
      Location:85 → 150
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      cl11519
      Location:1 → 53
      DENN; DENN (AEX-3) domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001105954.1: Suppressed sequence

      Description
      NM_001105954.1: This RefSeq was suppressed temporarily because the CDS was partial.
    Nucleotide Protein Strain
    Heading Accession and Version

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