U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Podnl1 podocan-like 1 [ Mus musculus (house mouse) ]

Gene ID: 244550, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
Podnl1provided by MGI
Official Full Name
podocan-like 1provided by MGI
Primary source
MGI:MGI:2685352
See related
Ensembl:ENSMUSG00000012889 AllianceGenome:MGI:2685352
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
Gm506; 5832418A03Rik
Summary
Located in collagen-containing extracellular matrix. Orthologous to human PODNL1 (podocan like 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in ovary adult (RPKM 13.5), spleen adult (RPKM 5.1) and 10 other tissues See more
Orthologs
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Podnl1 in Genome Data Viewer
Location:
8 C2; 8 40.31 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (84852552..84869620)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (84125928..84142991)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene regulatory factor X, 1 (influences HLA class II expression) Neighboring gene microRNA 709 Neighboring gene STARR-positive B cell enhancer mm9_chr8:86628640-86628941 Neighboring gene predicted gene, 39210 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86650788-86650941 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:86651237-86651346 Neighboring gene coiled-coil and C2 domain containing 1A Neighboring gene break repair meiotic recombinase recruitment factor 1 Neighboring gene nanos C2HC-type zinc finger 3 Neighboring gene microRNA 181d

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Podocan-like protein: a novel small leucine-rich repeat matrix protein in bone. Mochida Y, et al. Biochem Biophys Res Commun, 2011 Jul 1. PMID 21672516, Free PMC Article
  2. The developing mouse coronal suture at single-cell resolution. Farmer DT, et al. Nat Commun, 2021 Aug 10. PMID 34376651, Free PMC Article
  3. Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Kim H, et al. Cell, 2018 Dec 13. PMID 30550785, Free PMC Article
  4. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073
  5. High-efficiency full-length cDNA cloning. Carninci P, et al. Methods Enzymol, 1999. PMID 10349636

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. a novel SLRP member, "Podocan-like (Podnl) protein" identified by a bioinformatics approach was characterized.
    Title: Podocan-like protein: a novel small leucine-rich repeat matrix protein in bone.
Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1) 
  • Endonuclease-mediated (3) 

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Homology

Gene Ontology Provided by MGI

Component Evidence Code Pubs
located_in collagen-containing extracellular matrix IDA
Inferred from Direct Assay
more info
 PubMed 
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
  

General protein information

Go to the top of the page Help
Preferred Names
podocan-like protein 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_001013384.3 → NP_001013402.2  podocan-like protein 1 precursor

    See identical proteins and their annotated locations for NP_001013402.2

    Status: VALIDATED

    Source sequence(s)
    AC159266
    Consensus CDS
    CCDS52615.1
    UniProtKB/Swiss-Prot
    A0A0R4J142, A1X874, Q6P3Y9
    Related
    ENSMUSP00000091073.5, ENSMUST00000093380.5
    Conserved Domains (3) summary
    cd00116
    Location:161 → 345
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:211 → 234
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:210 → 271
    LRR_8; Leucine rich repeat

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_000074.7 Reference GRCm39 C57BL/6J

    Range
    84852552..84869620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011248377.3 → XP_011246679.1  podocan-like protein 1 isoform X1

    Conserved Domains (3) summary
    PRK15370
    Location:166 → 421
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00033
    Location:211 → 234
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:403 → 458
    LRR_8; Leucine rich repeat

  2. XM_011248378.1 → XP_011246680.1  podocan-like protein 1 isoform X2

    Conserved Domains (4) summary
    PRK15370
    Location:13 → 283
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:125 → 136
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:52 → 75
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:264 → 325
    LRR_8; Leucine rich repeat

  3. XM_017312815.3 → XP_017168304.1  podocan-like protein 1 isoform X2

    Conserved Domains (4) summary
    PRK15370
    Location:13 → 283
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:125 → 136
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:52 → 75
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:264 → 325
    LRR_8; Leucine rich repeat
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P3Y9.3 GenPept UniProtKB/Swiss-Prot:Q6P3Y9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous