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Pcdh15 protocadherin 15 [ Mus musculus (house mouse) ]

Gene ID: 11994, updated on 25-Nov-2021

Summary

Official Symbol
Pcdh15provided by MGI
Official Full Name
protocadherin 15provided by MGI
Primary source
MGI:MGI:1891428
See related
Ensembl:ENSMUSG00000052613
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
av; roda; Ush1f; nmf19; Gm9815; BB078305
Expression
Biased expression in frontal lobe adult (RPKM 1.4), CNS E18 (RPKM 1.1) and 9 other tissues See more
Orthologs
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Genomic context

See Pcdh15 in Genome Data Viewer
Location:
10 B5.3; 10 37.43 cM
Exon count:
49
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (72932003..74485663)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (73096277..74649831)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (73284615..74112482)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA A330049N07 gene Neighboring gene predicted gene, 34776 Neighboring gene heterogeneous nuclear ribonucleoprotein A2/B1 pseudogene Neighboring gene TPX2, microtubule-associated protein homolog pseudogene Neighboring gene ferritin light chain 1 pseudogene Neighboring gene predicted gene, 40691 Neighboring gene high mobility group box 1-like pseudogene Neighboring gene predicted gene 6419

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within actin filament bundle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within actin filament organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within adult locomotory behavior IMP
Inferred from Mutant Phenotype
more info
 
acts_upstream_of_or_within adult walking behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within auditory receptor cell stereocilium organization IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within auditory receptor cell stereocilium organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within detection of mechanical stimulus involved in equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in equilibrioception ISO
Inferred from Sequence Orthology
more info
 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within inner ear auditory receptor cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner ear development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inner ear receptor cell stereocilium organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within locomotory behavior IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within morphogenesis of an epithelium IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within non-motile cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in photoreceptor cell maintenance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within righting reflex IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sensory perception of light stimulus ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within sensory perception of sound IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within startle response IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within visual perception IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space ISO
Inferred from Sequence Orthology
more info
 
located_in integral component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in photoreceptor outer segment IDA
Inferred from Direct Assay
more info
PubMed 
located_in photoreceptor outer segment ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
is_active_in stereocilium EXP
Inferred from Experiment
more info
PubMed 
located_in stereocilium IDA
Inferred from Direct Assay
more info
PubMed 
located_in stereocilium bundle IDA
Inferred from Direct Assay
more info
PubMed 
located_in synapse ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
protocadherin-15
Names
Ames waltzer
protocadherin 15 CD2

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_001142735.1NP_001136207.1  protocadherin-15 isoform CD1-2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (B) lacks an alternate in-frame exon in the 5' coding region, compared to variant A. The resulting isoform (CD1-2), also known as protocadherin-15-CD1 isoform 2, lacks a 5-aa segment near the N-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354396
    Consensus CDS
    CCDS56715.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000101064.4, ENSMUST00000105424.10
    Conserved Domains (1) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
  2. NM_001142736.1NP_001136208.1  protocadherin-15 isoform CD1-4 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (C) lacks two alternate in-frame exons in the 5' and 3' coding region, compared to variant A. The resulting isoform (CD1-4), also known as protocadherin-15-CD1 isoform 4, lacks a 5-aa segment near the N-terminus and a 2-aa segment near the C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354398
    Consensus CDS
    CCDS56718.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000122911.3, ENSMUST00000131321.9
    Conserved Domains (1) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
  3. NM_001142737.1NP_001136209.1  protocadherin-15 isoform CD1-6 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (D) lacks an alternate in-frame exon in the 5' coding region and two alternate in-frame exons in the central coding region, compared to variant A. The resulting isoform (CD1-6), also known as protocadherin-15-CD1 isoform 6, lacks a 5-aa segment near the N-terminus and a 71-aa segment in the central protein, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354400
    Consensus CDS
    CCDS56719.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000101069.4, ENSMUST00000105429.10
    Conserved Domains (1) summary
    cd11304
    Location:651744
    Cadherin_repeat; Cadherin tandem repeat domain
  4. NM_001142738.1NP_001136210.1  protocadherin-15 isoform CD1-8 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (F) lacks 4 alternate in-frame exons, compared to variant A. The resulting isoform (CD1-8), also known as protocadherin-15-CD1 isoform 8, has the same N- and C-termini but lacks four internal segments, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354401
    Consensus CDS
    CCDS48595.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000122940.3, ENSMUST00000147189.9
    Conserved Domains (1) summary
    cd11304
    Location:685778
    Cadherin_repeat; Cadherin tandem repeat domain
  5. NM_001142739.1NP_001136211.1  protocadherin-15 isoform CD1-9 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (G) lacks two alternate in-frame exons in the 5' coding region, compared to variant A. The resulting isoform (CD1-9), also known as protocadherin-15-CD1 isoform 9, lacks a 27-aa segment near the N-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354402
    Consensus CDS
    CCDS56720.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000121939.3, ENSMUST00000126920.9
    Conserved Domains (1) summary
    cd11304
    Location:700793
    Cadherin_repeat; Cadherin tandem repeat domain
  6. NM_001142740.1NP_001136212.1  protocadherin-15 isoform CD1-7 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (E) lacks three alternate in-frame exons, compared to variant A. The resulting isoform (CD1-7), also known as protocadherin-15-CD1 isoform 7, has the same N- and C-termini but lacks three internal segments, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354403
    Consensus CDS
    CCDS48594.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000090076.7, ENSMUST00000092420.13
    Conserved Domains (1) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
  7. NM_001142741.1NP_001136213.1  protocadherin-15 isoform CD1-10 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (H) lacks three alternate in-frame exons, compared to variant A. The resulting isoform (CD1-10), also known as protocadherin-15-CD1 isoform 10, has the same N- and C-termini but lacks two internal segments, compared to isoform CD1-10.
    Source sequence(s)
    AC153858, AK139154, CJ166718, DQ354404
    Consensus CDS
    CCDS56721.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000117731.3, ENSMUST00000129404.9
    Conserved Domains (1) summary
    cd11304
    Location:700793
    Cadherin_repeat; Cadherin tandem repeat domain
  8. NM_001142742.1NP_001136214.1  protocadherin-15 isoform CD2-1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (I) includes an alternate in-frame exon in the central coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD2-1), also known as protocadherin-15-CD2 isoform 1, includes an alternate 7-aa segment in the central coding region and has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AK139154, CJ166718, DQ354405
    Consensus CDS
    CCDS56711.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000119662.3, ENSMUST00000151116.9
    Conserved Domains (1) summary
    cd11304
    Location:734827
    Cadherin_repeat; Cadherin tandem repeat domain
  9. NM_001142743.1NP_001136215.1  protocadherin-15 isoform CD2-2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (J) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD2-2), also known as protocadherin-15-CD2 isoform 2, lacks a 5-aa segment in the 5' coding region and has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AK139154, CJ166718, DQ354406
    Consensus CDS
    CCDS56716.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000122466.3, ENSMUST00000131724.9
    Conserved Domains (1) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
  10. NM_001142746.1NP_001136218.1  protocadherin-15 isoform CD3-1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (K) has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD3-1), also known as protocadherin-15-CD3 isoform 1, has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, CO433511, DQ354413
    Consensus CDS
    CCDS56713.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000135501.2, ENSMUST00000177107.8
    Conserved Domains (1) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
  11. NM_001142747.1NP_001136219.1  protocadherin-15 isoform SI-1 precursor

    See identical proteins and their annotated locations for NP_001136219.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (M) has a distinct 3' splice pattern, compared to variant A. The resulting isoform (SI-1), also known as protocadherin-15-secreted isoform 1, has a substantially shorter and distinct C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AK139154, CJ166718
    Consensus CDS
    CCDS56712.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000135849.2, ENSMUST00000177420.7
    Conserved Domains (1) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
  12. NM_001142748.1NP_001136220.1  protocadherin-15 isoform SI-2 precursor

    See identical proteins and their annotated locations for NP_001136220.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (N) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (SI-2), also known as protocadherin-15-secreted isoform 2, lacks a 5-aa segment near the N-terminus and has a substantially shorter and distinct C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    CJ166718, DQ354417
    Consensus CDS
    CCDS56714.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000120056.3, ENSMUST00000125006.9
    Conserved Domains (1) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
  13. NM_001142760.1NP_001136232.1  protocadherin-15 isoform CD3-2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (L) lacks an alternate in-frame exon in the 5' coding region and has a distinct 3' splice pattern, compared to variant A. The resulting isoform (CD3-2), also known as protocadherin-15-CD3 isoform 2, lacks a 5-aa segment near the N-terminus and has a distinct and longer C-terminus, compared to isoform CD1-1.
    Source sequence(s)
    AC153858, AK139154, CJ166718, CO433511, DQ354414
    Consensus CDS
    CCDS56717.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000141973.2, ENSMUST00000191854.6
    Conserved Domains (1) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
  14. NM_023115.3NP_075604.2  protocadherin-15 isoform CD1-1 precursor

    See identical proteins and their annotated locations for NP_075604.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (A) encodes isoform CD1-1, also known as protocadherin-15-CD1 isoform 1.
    Source sequence(s)
    AC121142, AC153858, AF281899, CJ166718
    Consensus CDS
    CCDS35934.1
    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000141792.2, ENSMUST00000193361.6
    Conserved Domains (1) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    72932003..74485663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017313785.3XP_017169274.1  protocadherin-15 isoform X7

    Conserved Domains (2) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam18432
    Location:36145
    ECD; Extracellular Cadherin domain
  2. XM_017313784.3XP_017169273.1  protocadherin-15 isoform X1

    Related
    ENSMUSP00000141920.2, ENSMUST00000195531.6
    Conserved Domains (2) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam18432
    Location:36145
    ECD; Extracellular Cadherin domain
  3. XM_006513155.5XP_006513218.1  protocadherin-15 isoform X2

    Conserved Domains (2) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam18432
    Location:36145
    ECD; Extracellular Cadherin domain
  4. XM_006513156.5XP_006513219.1  protocadherin-15 isoform X3

    UniProtKB/Swiss-Prot
    Q99PJ1
    Related
    ENSMUSP00000142173.2, ENSMUST00000193739.6
    Conserved Domains (2) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam18432
    Location:36145
    ECD; Extracellular Cadherin domain
  5. XM_036155565.1XP_036011458.1  protocadherin-15 isoform X5

    Conserved Domains (3) summary
    cd11304
    Location:727820
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:310398
    CA; Cadherin repeats
    pfam18432
    Location:36145
    ECD; Extracellular Cadherin domain
  6. XM_036155566.1XP_036011459.1  protocadherin-15 isoform X6

    Conserved Domains (3) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:305393
    CA; Cadherin repeats
    pfam18432
    Location:31140
    ECD; Extracellular Cadherin domain
  7. XM_036155564.1XP_036011457.1  protocadherin-15 isoform X4

    Conserved Domains (3) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:305393
    CA; Cadherin repeats
    pfam18432
    Location:31140
    ECD; Extracellular Cadherin domain
  8. XM_036155563.1XP_036011456.1  protocadherin-15 isoform X4

    Conserved Domains (3) summary
    cd11304
    Location:722815
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:305393
    CA; Cadherin repeats
    pfam18432
    Location:31140
    ECD; Extracellular Cadherin domain

RNA

  1. XR_004936069.1 RNA Sequence

  2. XR_004936071.1 RNA Sequence

  3. XR_004936081.1 RNA Sequence

  4. XR_004936073.1 RNA Sequence

  5. XR_004936072.1 RNA Sequence

  6. XR_004936089.1 RNA Sequence

  7. XR_004936068.1 RNA Sequence

  8. XR_001779426.3 RNA Sequence

  9. XR_004936076.1 RNA Sequence

  10. XR_004936086.1 RNA Sequence

  11. XR_004936077.1 RNA Sequence

  12. XR_004936087.1 RNA Sequence

  13. XR_004936078.1 RNA Sequence

  14. XR_004936083.1 RNA Sequence

  15. XR_004936080.1 RNA Sequence

  16. XR_004936088.1 RNA Sequence

  17. XR_004936093.1 RNA Sequence

  18. XR_004936074.1 RNA Sequence

  19. XR_004936092.1 RNA Sequence

  20. XR_004936075.1 RNA Sequence

  21. XR_004936070.1 RNA Sequence

  22. XR_004936082.1 RNA Sequence

  23. XR_004936091.1 RNA Sequence

  24. XR_004936079.1 RNA Sequence

  25. XR_004936084.1 RNA Sequence

  26. XR_004936085.1 RNA Sequence

  27. XR_004936090.1 RNA Sequence

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