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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)

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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_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