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

Gene ID: 116741, updated on 2-May-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
Ensembl: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 integral component of plasma membrane. Orthologous to several human genes including PCDHA4 (protocadherin alpha 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 146.0), Lung (RPKM 106.0) and 8 other tissues See more
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Genomic context

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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 cell differentiation IEA
Inferred from Electronic Annotation
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
protocadherin alpha c2

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
    Related
    ENSRNOP00000075260.2, ENSRNOT00000079794.2
    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

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

    UniProtKB/TrEMBL
    A6J343, E9PSN7, Q767J1
    Related
    ENSRNOP00000027402.4
    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
    M0R8Z9, Q767J0

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

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

    UniProtKB/TrEMBL
    M0RBC1, Q767I9
    Related
    ENSRNOP00000066853.2
    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
    Related
    ENSRNOP00000027393.6
    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

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

    UniProtKB/TrEMBL
    F7F4E7, I6LBW5, Q767I6
    Related
    ENSRNOP00000027383.6
    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

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

    UniProtKB/TrEMBL
    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
    Related
    ENSRNOP00000074100.1
    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

  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
    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

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