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    Pcdha4 protocadherin alpha 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 116741, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Pcdha4provided by RGD
    Official Full Name
    protocadherin alpha 4provided by RGD
    Primary source
    RGD:620337
    See related
    EnsemblRapid:ENSRNOG00000020119 AllianceGenome:RGD:620337
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Cnr1; cnr5; Pcdha1; Pcdha2; Pcdha3; Pcdha5; Pcdha6; Pcdha7; Pcdha8; Pcdha9; Pcdha10; Pcdha11; Pcdha12; Pcdha13; Pcdhac1; Pcdhac2; rCNRv01; rCNRv02; rCNRv03; rCNRv05; rCNRv06; rCNRv07; rCNRv08; rCNRv09; rCNRv10; rCNRv11; rCNRv12; rCNRv13; rCNRvc1; rCNRvc2
    Summary
    Predicted to enable calcium ion binding activity and identical protein binding activity. Predicted to be involved in cell adhesion. Predicted to be located in endoplasmic reticulum; membrane; and synapse. Predicted to be active in plasma membrane. Orthologous to human PCDHA4 (protocadherin alpha 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 146.0), Lung (RPKM 106.0) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pcdha4 in Genome Data Viewer
    Location:
    18p11
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (28688274..29120227)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (28581040..28846214)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (29950217..30215901)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene histidyl-tRNA synthetase 2, mitochondrial Neighboring gene zinc finger, matrin type 2 Neighboring gene zinc finger protein 260, pseudogene 1 Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC120098168 Neighboring gene uncharacterized LOC134482930 Neighboring gene ATP synthase F(0) complex subunit C1, mitochondrial-like Neighboring gene protocadherin beta 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Protocadherin alpha3 acts at sites distinct from classic cadherins in rat testis and sperm. Johnson KJ, et al. Biol Reprod, 2004 Feb. PMID 14522826
    2. Cadherin-related neuronal receptors in incisor development. Fukumoto E, et al. J Dent Res, 2003 Jan. PMID 12508039
    3. Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins. Goodman KM, et al. Neuron, 2016 May 18. PMID 27161523, Free PMC Article
    4. Two novel CNRs from the CNR gene cluster have molecular features distinct from those of CNR1 to 8. Takei Y, et al. Genomics, 2001 Mar 15. PMID 11401448
    5. Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex. Kohmura N, et al. Neuron, 1998 Jun. PMID 9655502

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC93781

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calcium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin alpha-4
    Names
    PCDH-alpha-4
    cadherin-related neuronal receptor 1
    cadherin-related neuronal receptor 10
    cadherin-related neuronal receptor 11
    cadherin-related neuronal receptor 12
    cadherin-related neuronal receptor 13
    cadherin-related neuronal receptor 2
    cadherin-related neuronal receptor 3
    cadherin-related neuronal receptor 4
    cadherin-related neuronal receptor 5
    cadherin-related neuronal receptor 6
    cadherin-related neuronal receptor 7
    cadherin-related neuronal receptor 8
    cadherin-related neuronal receptor 9
    cadherin-related neuronal receptor c1
    cadherin-related neuronal receptor c2
    protocadherin alpha 1
    protocadherin alpha 10
    protocadherin alpha 11
    protocadherin alpha 12
    protocadherin alpha 13
    protocadherin alpha 2
    protocadherin alpha 3
    protocadherin alpha 5
    protocadherin alpha 6
    protocadherin alpha 7
    protocadherin alpha 8
    protocadherin alpha 9
    protocadherin alpha c1

    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_053933.2 → NP_446385.1  protocadherin alpha-4 precursor

      See identical proteins and their annotated locations for NP_446385.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/Swiss-Prot
      Q5U2Z9, Q767I8, Q8CJ01
      UniProtKB/TrEMBL
      Q593X7
      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 → 939
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086036.1 Reference GRCr8

      Range
      28688274..29120227
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063277068.1 → XP_063133138.1  protocadherin alpha-4 isoform X20

      UniProtKB/TrEMBL
      A6J343

    2. XM_017600822.3 → XP_017456311.1  protocadherin alpha-4 isoform X11

      UniProtKB/TrEMBL
      A6J343, E9PSN7, Q767J1
      Related
      ENSRNOP00000027402.4, ENSRNOT00000027402.5
      Conserved Domains (3) summary
      cd11304
      Location:247 → 347
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 112
      Cadherin_2; Cadherin-like
      pfam15974
      Location:797 → 940
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    3. XM_063277061.1 → XP_063133131.1  protocadherin alpha-4 isoform X10

      UniProtKB/TrEMBL
      A0A8J8XGC7, M0R8Z9, Q767J0

    4. XM_063277067.1 → XP_063133137.1  protocadherin alpha-4 isoform X19

      UniProtKB/TrEMBL
      A0A8J8XGC7

    5. XM_017600825.3 → XP_017456314.1  protocadherin alpha-4 isoform X14

      UniProtKB/TrEMBL
      M0RBC1, Q767I9
      Conserved Domains (3) summary
      cd11304
      Location:244 → 343
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:27 → 108
      Cadherin_2; Cadherin-like
      pfam15974
      Location:791 → 934
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    6. XM_017600827.3 → XP_017456316.1  protocadherin alpha-4 isoform X16

      UniProtKB/TrEMBL
      A6J347, Q767I7
      Conserved Domains (3) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:783 → 926
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    7. XM_063277065.1 → XP_063133135.1  protocadherin alpha-4 isoform X17

      UniProtKB/TrEMBL
      I6LBW5

    8. XM_017600817.3 → XP_017456306.1  protocadherin alpha-4 isoform X5

      UniProtKB/TrEMBL
      F7F4E7, I6LBW5, Q767I6
      Related
      ENSRNOP00000027383.6, ENSRNOT00000027383.8
      Conserved Domains (4) summary
      cd11304
      Location:263 → 363
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:47 → 128
      Cadherin_2; Cadherin-like
      pfam15974
      Location:812 → 955
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:711 → 786
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    9. XM_063277064.1 → XP_063133134.1  protocadherin alpha-4 isoform X15

      UniProtKB/TrEMBL
      M0RB51, Q767I5

    10. XM_063277060.1 → XP_063133130.1  protocadherin alpha-4 isoform X9

      UniProtKB/TrEMBL
      F7F4G8, Q767I4
      Related
      ENSRNOP00000027372.7, ENSRNOT00000027372.8

    11. XM_063277063.1 → XP_063133133.1  protocadherin alpha-4 isoform X13

      UniProtKB/TrEMBL
      A6J351, F1LM35, Q767I3

    12. XM_017600816.3 → XP_017456305.1  protocadherin alpha-4 isoform X4

      UniProtKB/TrEMBL
      Q767I2
      Conserved Domains (3) summary
      cd11304
      Location:276 → 376
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:60 → 141
      Cadherin_2; Cadherin-like
      pfam15974
      Location:828 → 971
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    13. XM_017600823.3 → XP_017456312.1  protocadherin alpha-4 isoform X12

      UniProtKB/TrEMBL
      Q767I1
      Conserved Domains (3) summary
      cd11304
      Location:247 → 347
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 112
      Cadherin_2; Cadherin-like
      pfam15974
      Location:796 → 939
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    14. XM_017600818.3 → XP_017456307.1  protocadherin alpha-4 isoform X8

      UniProtKB/TrEMBL
      Q593Y1, Q767I0
      Conserved Domains (3) summary
      cd11304
      Location:246 → 345
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:799 → 942
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    15. XM_017600819.3 → XP_017456308.1  protocadherin alpha-4 isoform X7

      UniProtKB/TrEMBL
      A0A0G2K783, I6LBW4, Q767H9
      Conserved Domains (3) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:799 → 942
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    16. XM_063277066.1 → XP_063133136.1  protocadherin alpha-4 isoform X18

      UniProtKB/TrEMBL
      Q767H9

    17. XM_039096548.2 → XP_038952476.1  protocadherin alpha-4 isoform X21

      Conserved Domains (3) summary
      cd11304
      Location:246 → 346
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:30 → 111
      Cadherin_2; Cadherin-like
      pfam15974
      Location:536 → 678
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    18. XM_063277056.1 → XP_063133126.1  protocadherin alpha-4 isoform X1

    19. XM_063277057.1 → XP_063133127.1  protocadherin alpha-4 isoform X2

    20. XM_017600815.3 → XP_017456304.1  protocadherin alpha-4 isoform X3

      UniProtKB/TrEMBL
      Q767H7
      Related
      ENSRNOP00000027340.3, ENSRNOT00000027340.7
      Conserved Domains (4) summary
      cd11304
      Location:260 → 360
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam15974
      Location:855 → 998
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:702 → 807
      Cadherin_C_2; Cadherin cytoplasmic C-terminal
      cl09101
      Location:42 → 126
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    21. XM_063277059.1 → XP_063133129.1  protocadherin alpha-4 isoform X6

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q767I8.1 GenPept UniProtKB/Swiss-Prot:Q767I8

    Gene LinkOut

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