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    Vps13b vacuolar protein sorting 13 homolog B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315036, updated on 9-Dec-2024

    Summary

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    Symbol
    Vps13bprovided by RGD
    Full Name
    vacuolar protein sorting 13 homolog Bprovided by RGD
    Primary source
    RGD:1311183
    See related
    EnsemblRapid:ENSRNOG00000066252 AllianceGenome:RGD:1311183
    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
    Coh1; Cohh1
    Summary
    Predicted to enable phosphatidylinositol-3-phosphate binding activity. Predicted to be involved in several processes, including acrosome assembly; maintenance of lens transparency; and slow endocytic recycling. Predicted to act upstream of or within several processes, including dentate gyrus development; head morphogenesis; and social behavior. Predicted to be located in Golgi apparatus and bounding membrane of organelle. Human ortholog(s) of this gene implicated in Cohen syndrome. Orthologous to human VPS13B (vacuolar protein sorting 13 homolog B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 193.2), Thymus (RPKM 192.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps13b in Genome Data Viewer
    Location:
    7q22
    Exon count:
    72
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (68436996..69013574)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (66557862..67128429)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (74118834..74722341)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene odd-skipped related transciption factor 2 Neighboring gene ubiquitin A-52 residue ribosomal protein fusion product 1, pseudogene 2 Neighboring gene pre-mRNA-splicing factor SPF27 pseudogene Neighboring gene ATM interactor, pseudogene 2 Neighboring gene microRNA 875 Neighboring gene pre-mRNA-splicing factor CWC22 homolog Neighboring gene cytochrome c oxidase subunit 6C

    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. Cohen syndrome is caused by mutations in a novel gene, COH1, encoding a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport. Kolehmainen J, et al. Am J Hum Genet, 2003 Jun. PMID 12730828, Free PMC Article
    2. Gene and alternative splicing annotation with AIR. Florea L, et al. Genome Res, 2005 Jan. PMID 15632090, 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 phosphatidylinositol-3-phosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in Golgi reassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in acrosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in adipose tissue development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in central nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within dentate gyrus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within head morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in maintenance of lens transparency ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within memory ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within multicellular organism growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within muscle organ development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in slow endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within social behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in acrosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cis-Golgi network membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in trans-Golgi network membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    intermembrane lipid transfer protein VPS13B
    Names
    Cohen syndrome homolog 1
    vacuolar protein sorting-associated protein 13B
    vacuolar protein sorting-associated protein 13B-like

    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_001134886.2 → NP_001128358.1  intermembrane lipid transfer protein VPS13B

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A8I5Y7Q0
      Related
      ENSRNOP00000077378.2, ENSRNOT00000105415.2
      Conserved Domains (4) summary
      pfam06650
      Location:2606 → 2686
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3707 → 3811
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:3 → 94
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:3559 → 3705
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    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_086025.1 Reference GRCr8

      Range
      68436996..69013574
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039079215.2 → XP_038935143.1  intermembrane lipid transfer protein VPS13B isoform X1

      Conserved Domains (4) summary
      pfam06650
      Location:2605 → 2685
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3717 → 3810
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:6 → 94
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:3558 → 3704
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    2. XM_039079218.2 → XP_038935146.1  intermembrane lipid transfer protein VPS13B isoform X3

      UniProtKB/TrEMBL
      A0A8I6AM06
      Related
      ENSRNOP00000094909.1, ENSRNOT00000114232.2
      Conserved Domains (4) summary
      pfam06650
      Location:2503 → 2583
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3615 → 3708
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:6 → 94
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:3456 → 3602
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    3. XM_039079219.2 → XP_038935147.1  intermembrane lipid transfer protein VPS13B isoform X4

      Conserved Domains (4) summary
      pfam06650
      Location:2502 → 2582
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3614 → 3707
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:6 → 94
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:3455 → 3601
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    4. XM_039079221.2 → XP_038935149.1  intermembrane lipid transfer protein VPS13B isoform X7

      UniProtKB/TrEMBL
      A0A8I6AKJ7
      Related
      ENSRNOP00000093776.1, ENSRNOT00000094539.2
      Conserved Domains (2) summary
      pfam06650
      Location:2606 → 2686
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam12624
      Location:6 → 94
      Chorein_N; N-terminal region of Chorein or VPS13

    5. XM_039079224.2 → XP_038935152.1  intermembrane lipid transfer protein VPS13B isoform X12

      Conserved Domains (1) summary
      pfam12624
      Location:6 → 94
      Chorein_N; N-terminal region of Chorein or VPS13

    6. XM_063263570.1 → XP_063119640.1  intermembrane lipid transfer protein VPS13B isoform X13

    7. XM_063263572.1 → XP_063119642.1  intermembrane lipid transfer protein VPS13B isoform X15

    8. XM_063263571.1 → XP_063119641.1  intermembrane lipid transfer protein VPS13B isoform X14

    9. XM_063263573.1 → XP_063119643.1  intermembrane lipid transfer protein VPS13B isoform X16

    10. XM_063263574.1 → XP_063119644.1  intermembrane lipid transfer protein VPS13B isoform X17

    11. XM_063263575.1 → XP_063119645.1  intermembrane lipid transfer protein VPS13B isoform X18

    12. XM_039079216.2 → XP_038935144.1  intermembrane lipid transfer protein VPS13B isoform X2

      Conserved Domains (3) summary
      pfam06650
      Location:2557 → 2637
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3669 → 3762
      ATG_C; Autophagy-related protein C terminal domain
      pfam16909
      Location:3510 → 3656
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    13. XM_063263566.1 → XP_063119636.1  intermembrane lipid transfer protein VPS13B isoform X5

    14. XM_039079220.2 → XP_038935148.1  intermembrane lipid transfer protein VPS13B isoform X6

      Conserved Domains (3) summary
      pfam06650
      Location:2334 → 2414
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3446 → 3539
      ATG_C; Autophagy-related protein C terminal domain
      pfam16909
      Location:3287 → 3433
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    15. XM_063263567.1 → XP_063119637.1  intermembrane lipid transfer protein VPS13B isoform X8

    16. XM_063263568.1 → XP_063119638.1  intermembrane lipid transfer protein VPS13B isoform X9

    17. XM_039079222.2 → XP_038935150.1  intermembrane lipid transfer protein VPS13B isoform X10

      Conserved Domains (3) summary
      pfam06650
      Location:879 → 959
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:1991 → 2084
      ATG_C; Autophagy-related protein C terminal domain
      pfam16909
      Location:1832 → 1978
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    18. XM_039079223.2 → XP_038935151.1  intermembrane lipid transfer protein VPS13B isoform X11

      Conserved Domains (3) summary
      pfam06650
      Location:868 → 948
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:1980 → 2073
      ATG_C; Autophagy-related protein C terminal domain
      pfam16909
      Location:1821 → 1967
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    RNA

    1. XR_010052974.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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