Podn podocan [Mus musculus (house mouse)] - Gene

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, Nov 2024]
Expression: Broad expression in duodenum adult (RPKM 27.1), bladder adult (RPKM 26.4) and 17 other tissues See more
Orthologs: human all
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Genomic context

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_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Podocan promoting skeletal muscle post-injury regeneration by inhibiting TGF-beta signaling pathway.
Title: Podocan promoting skeletal muscle post-injury regeneration by inhibiting TGF-β signaling pathway.
Podn was characterized in cultured mouse cells.
Title: Functional characterization of podocan, a member of a new class in the small leucine-rich repeat protein family.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (4) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables collagen binding	IEA Inferred from Electronic Annotation more info
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 migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: podocan

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)

NM_001285956.2 → NP_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:71 → 309

PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP

PLN00113
Location:119 → 583

PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional

sd00033
Location:123 → 148

LRR_RI; leucine-rich repeat [structural motif]
NM_001285958.2 → NP_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:71 → 309

PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP

PLN00113
Location:119 → 583

PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional

sd00033
Location:123 → 148

LRR_RI; leucine-rich repeat [structural motif]
NM_001425123.1 → NP_001412052.1 podocan precursor

Status: VALIDATED

Source sequence(s)

AL611936

UniProtKB/Swiss-Prot

A2A8F3, Q7TQ62, Q8BM45
NM_001425124.1 → NP_001412053.1 podocan precursor

Status: VALIDATED

Source sequence(s)

AL611936

UniProtKB/Swiss-Prot

A2A8F3, Q7TQ62, Q8BM45
NM_172874.4 → NP_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:71 → 309

PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP

PLN00113
Location:119 → 583

PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional

sd00033
Location:123 → 148

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

NC_000070.7 Reference GRCm39 C57BL/6J

Range

107871990..107889544 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030253568.1 → XP_030109428.1 podocan isoform X2

Conserved Domains (3) summary

PRK15370
Location:18 → 329

PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP

sd00033
Location:29 → 52

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:312 → 371

LRR_8; Leucine rich repeat
XM_011240532.1 → XP_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:18 → 329

PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP

sd00033
Location:29 → 52

LRR_RI; leucine-rich repeat [structural motif]

pfam13855
Location:312 → 371

LRR_8; Leucine rich repeat