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Pcdha4b protocadherin alpha 4B [ Mus musculus (house mouse) ]

Gene ID: 100384868, updated on 2-Nov-2024

Summary

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Official Symbol
Pcdha4bprovided by MGI
Official Full Name
protocadherin alpha 4Bprovided by MGI
Primary source
MGI:MGI:5610241
See related
Ensembl:ENSMUSG00000103458 AllianceGenome:MGI:5610241
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
Cnr1; Pcdha4; Gm37013; Pcdha4-g
Summary
Orthologous to human PCDHA4 (protocadherin alpha 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in frontal lobe adult (RPKM 48.5), whole brain E14.5 (RPKM 44.1) and 24 other tissues See more
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Genomic context

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See Pcdha4b in Genome Data Viewer
Location:
18 B2- B3; 18
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (37085701..37974926)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (36952648..37841873)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr18:36962302-36962603 Neighboring gene STARR-positive B cell enhancer ABC_E1207 Neighboring gene STARR-seq mESC enhancer starr_44299 Neighboring gene STARR-seq mESC enhancer starr_44300 Neighboring gene STARR-seq mESC enhancer starr_44301 Neighboring gene vault RNA component 5 Neighboring gene STARR-seq mESC enhancer starr_44302 Neighboring gene STARR-seq mESC enhancer starr_44303 Neighboring gene STARR-seq mESC enhancer starr_44304 Neighboring gene STARR-seq mESC enhancer starr_44305 Neighboring gene 3-phosphoglycerate dehydrogenase pseudogene Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene predicted gene, 38666 Neighboring gene protocadherin alpha 5 Neighboring gene predicted gene, 38667 Neighboring gene predicted gene, 36858 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 11 Neighboring gene predicted gene 10545 Neighboring gene protocadherin alpha 5 pseudogene Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 12 Neighboring gene heat shock transcription factor 2 binding protein pseudogene Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene predicted gene 10544 Neighboring gene STARR-seq mESC enhancer starr_44309 Neighboring gene protocadherin beta 1 Neighboring gene RAD18 homolog pseudogene Neighboring gene protocadherin beta 2 Neighboring gene protocadherin beta 3 Neighboring gene protocadherin beta 4 Neighboring gene protocadherin beta 5 Neighboring gene protocadherin beta 6 Neighboring gene protocadherin beta 7 Neighboring gene protocadherin beta 8 Neighboring gene protocadherin beta 10 Neighboring gene protocadherin beta 9 Neighboring gene protocadherin beta 11 Neighboring gene predicted gene, 20162 Neighboring gene protocadherin beta 12 Neighboring gene protocadherin beta 13 Neighboring gene protocadherin beta 14 Neighboring gene STARR-seq mESC enhancer starr_44310 Neighboring gene protocadherin beta 15 Neighboring gene STARR-seq mESC enhancer starr_44311 Neighboring gene protocadherin beta 16 Neighboring gene protocadherin beta 17 Neighboring gene protocadherin beta 18 Neighboring gene protocadherin beta 19 Neighboring gene STARR-seq mESC enhancer starr_44313 Neighboring gene protocadherin beta 20 Neighboring gene protocadherin beta 21 Neighboring gene protocadherin beta 22 Neighboring gene STARR-seq mESC enhancer starr_44314 Neighboring gene RIKEN cDNA 3222401L13 gene Neighboring gene STARR-positive B cell enhancer ABC_E4245 Neighboring gene STARR-seq mESC enhancer starr_44317 Neighboring gene solute carrier family 25 (mitochondrial carrier, ornithine transporter) member 2 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protein UXT pseudogene Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene STARR-seq mESC enhancer starr_44321 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene predicted gene, 24401 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene STARR-seq mESC enhancer starr_44322 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene STARR-seq mESC enhancer starr_44324 Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene protocadherin gamma subfamily B, 8 Neighboring gene cDNA sequence BC037039 Neighboring gene STARR-seq mESC enhancer starr_44330 Neighboring gene STARR-seq mESC enhancer starr_44331 Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene STARR-seq mESC enhancer starr_44332 Neighboring gene predicted gene, 29994 Neighboring gene STARR-positive B cell enhancer ABC_E8711 Neighboring gene STARR-seq mESC enhancer starr_44334 Neighboring gene STARR-positive B cell enhancer ABC_E1953 Neighboring gene microRNA 6979 Neighboring gene diaphanous related formin 1 Neighboring gene histone deacetylase 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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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Related articles in PubMed

  1. Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model. Wang X, et al. Genes Dev, 2002 Aug 1. PMID 12154121, Free PMC Article
  2. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

General protein information

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Preferred Names
protocadherin alpha 4-gamma
Names
PCDH-alpha-4
Protocadherin alpha-4

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_001174154.2 → NP_001167625.1  protocadherin alpha 4-gamma precursor

    See identical proteins and their annotated locations for NP_001167625.1

    Status: VALIDATED

    Source sequence(s)
    AC020968, AC129315, AF464175
    UniProtKB/Swiss-Prot
    O88689
    UniProtKB/TrEMBL
    Q8K492
    Related
    ENSMUSP00000111325.4, ENSMUST00000115661.5
    Conserved Domains (3) summary
    cd11304
    Location:247 → 346
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:30 → 111
    Cadherin_2; Cadherin-like
    pfam15974
    Location:796 → 892
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

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_000084.7 Reference GRCm39 C57BL/6J

    Range
    37085701..37974926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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