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    Podn podocan [ Mus musculus (house mouse) ]

    Gene ID: 242608, updated on 12-May-2024

    Summary

    Official Symbol
    Podnprovided by MGI
    Official Full Name
    podocanprovided by MGI
    Primary source
    MGI:MGI:2674939
    See related
    Ensembl:ENSMUSG00000028600 AllianceGenome:MGI:2674939
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Pcan; SLRR5A; 9430070G18
    Summary
    Predicted to enable collagen binding activity. Predicted to be involved in negative regulation of cell migration and negative regulation of cell population proliferation. Predicted to be located in cytoplasm. Predicted to be active in extracellular space. Is expressed in several structures, including alimentary system; brain; limb; skeleton; and urinary system. Orthologous to human PODN (podocan). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in duodenum adult (RPKM 27.1), bladder adult (RPKM 26.4) and 17 other tissues See more
    Orthologs
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    Genomic context

    See Podn in Genome Data Viewer
    Location:
    4 C7; 4 50.18 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (107871990..107889544, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (108014793..108031954, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 4930407G08 gene Neighboring gene solute carrier family 1 (glutamate transporter), member 7 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:107690940-107691141 Neighboring gene predicted gene, 23354 Neighboring gene sterol carrier protein 2, liver Neighboring gene STARR-positive B cell enhancer ABC_E9592 Neighboring gene STARR-seq mESC enhancer starr_11029 Neighboring gene microRNA 6397

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (4)  1 citation

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables collagen binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in negative regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001285956.2NP_001272885.1  podocan precursor

      See identical proteins and their annotated locations for NP_001272885.1

      Status: VALIDATED

      Source sequence(s)
      AL611936
      Consensus CDS
      CCDS18445.1
      UniProtKB/Swiss-Prot
      A2A8F3, Q7TQ62, Q8BM45
      Conserved Domains (3) summary
      PRK15370
      Location:71309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123148
      LRR_RI; leucine-rich repeat [structural motif]
    2. NM_001285958.2NP_001272887.1  podocan precursor

      See identical proteins and their annotated locations for NP_001272887.1

      Status: VALIDATED

      Source sequence(s)
      AL611936
      Consensus CDS
      CCDS18445.1
      UniProtKB/Swiss-Prot
      A2A8F3, Q7TQ62, Q8BM45
      Related
      ENSMUSP00000102319.2, ENSMUST00000106708.8
      Conserved Domains (3) summary
      PRK15370
      Location:71309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123148
      LRR_RI; leucine-rich repeat [structural motif]
    3. NM_001425123.1NP_001412052.1  podocan precursor

      Status: VALIDATED

      Source sequence(s)
      AL611936
      UniProtKB/Swiss-Prot
      A2A8F3, Q7TQ62, Q8BM45
    4. NM_001425124.1NP_001412053.1  podocan precursor

      Status: VALIDATED

      Source sequence(s)
      AL611936
      UniProtKB/Swiss-Prot
      A2A8F3, Q7TQ62, Q8BM45
    5. NM_172874.4NP_766462.2  podocan precursor

      See identical proteins and their annotated locations for NP_766462.2

      Status: VALIDATED

      Source sequence(s)
      AL611936
      Consensus CDS
      CCDS18445.1
      UniProtKB/Swiss-Prot
      A2A8F3, Q7TQ62, Q8BM45
      Related
      ENSMUSP00000102320.3, ENSMUST00000106709.9
      Conserved Domains (3) summary
      PRK15370
      Location:71309
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:119583
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:123148
      LRR_RI; leucine-rich repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      107871990..107889544 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030253568.1XP_030109428.1  podocan isoform X2

      Conserved Domains (3) summary
      PRK15370
      Location:18329
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:2952
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:312371
      LRR_8; Leucine rich repeat
    2. XM_011240532.1XP_011238834.1  podocan isoform X2

      See identical proteins and their annotated locations for XP_011238834.1

      UniProtKB/Swiss-Prot
      Q7TQ62
      Conserved Domains (3) summary
      PRK15370
      Location:18329
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:2952
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:312371
      LRR_8; Leucine rich repeat