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    Focad focadhesin [ Mus musculus (house mouse) ]

    Gene ID: 230393, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Focadprovided by MGI
    Official Full Name
    focadhesinprovided by MGI
    Primary source
    MGI:MGI:2676921
    See related
    Ensembl:ENSMUSG00000038368 AllianceGenome:MGI:2676921
    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
    Summary
    Predicted to be involved in regulation of post-transcriptional gene silencing. Predicted to be located in focal adhesion. Is expressed in cranium; diencephalon lateral wall ventricular layer; and midbrain ventricular layer. Orthologous to human FOCAD (focadhesin). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in frontal lobe adult (RPKM 3.5), cortex adult (RPKM 3.3) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Focad in Genome Data Viewer
    Location:
    4 C4; 4 41.4 cM
    Exon count:
    48
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (88012858..88329248)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (88094620..88411011)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34180 Neighboring gene STARR-seq mESC enhancer starr_10714 Neighboring gene STARR-seq mESC enhancer starr_10715 Neighboring gene STARR-seq mESC enhancer starr_10716 Neighboring gene STARR-seq mESC enhancer starr_10718 Neighboring gene myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3 Neighboring gene STARR-positive B cell enhancer mm9_chr4:87680226-87680527 Neighboring gene predicted gene, 34232 Neighboring gene STARR-positive B cell enhancer mm9_chr4:87681371-87681672 Neighboring gene STARR-seq mESC enhancer starr_10719 Neighboring gene STARR-positive B cell enhancer ABC_E8809 Neighboring gene STARR-seq mESC enhancer starr_10720 Neighboring gene STARR-seq mESC enhancer starr_10721 Neighboring gene microRNA 491 Neighboring gene STARR-seq mESC enhancer starr_10722 Neighboring gene STARR-seq mESC enhancer starr_10723 Neighboring gene 3-hydroxyacyl-CoA dehydratase 4 Neighboring gene STARR-seq mESC enhancer starr_10724 Neighboring gene interferon beta 1, fibroblast Neighboring gene interferon alpha 15

    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
    • 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. PRICKLE1 × FOCAD Interaction Revealed by Genome-Wide vQTL Analysis of Human Facial Traits. Liu D, et al. Front Genet, 2021. PMID 34434215, Free PMC Article
    2. Chromatin Remodeling BAF155 Subunit Regulates the Genesis of Basal Progenitors in Developing Cortex. Narayanan R, et al. iScience, 2018 Jun 29. PMID 30240734, Free PMC Article
    3. Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Feb 28. PMID 12693553
    4. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article
    5. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • KIAA1797

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in regulation of post-transcriptional gene silencing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in focal adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in focal adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    focadhesin

    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_001081184.2 → NP_001074653.1  focadhesin isoform 1

      See identical proteins and their annotated locations for NP_001074653.1

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL772316, AL831756, BX572638
      Consensus CDS
      CCDS38798.1
      UniProtKB/Swiss-Prot
      A2AKG8, Q0P620, Q3TPY9, Q3UJY8, Q3UK73, Q6PGE3
      Related
      ENSMUSP00000095602.4, ENSMUST00000097992.10
      Conserved Domains (2) summary
      pfam11229
      Location:1210 → 1798
      DUF3028; Protein of unknown function (DUF3028)
      pfam12530
      Location:490 → 714
      DUF3730; Protein of unknown function (DUF3730)

    2. NM_001419409.1 → NP_001406338.1  focadhesin isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL772316, AL831756, BX572638
      UniProtKB/TrEMBL
      E9PYJ6
      Related
      ENSMUSP00000124298.2, ENSMUST00000159342.8

    3. NM_001419410.1 → NP_001406339.1  focadhesin isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL772316, AL831756, BX572638

    4. NM_001419411.1 → NP_001406340.1  focadhesin isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL831756

    5. NM_001419412.1 → NP_001406341.1  focadhesin isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL831756

    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_000070.7 Reference GRCm39 C57BL/6J

      Range
      88012858..88329248
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030253421.2 → XP_030109281.1  focadhesin isoform X3

      Conserved Domains (2) summary
      pfam11229
      Location:1127 → 1715
      Focadhesin
      pfam12530
      Location:407 → 631
      DUF3730; Protein of unknown function (DUF3730)

    2. XM_036164001.1 → XP_036019894.1  focadhesin isoform X8

      Conserved Domains (1) summary
      pfam12530
      Location:528 → 752
      DUF3730; Protein of unknown function (DUF3730)

    3. XM_006537886.4 → XP_006537949.1  focadhesin isoform X9

      Conserved Domains (1) summary
      pfam12530
      Location:528 → 752
      DUF3730; Protein of unknown function (DUF3730)

    4. XM_006537885.5 → XP_006537948.1  focadhesin isoform X7

      Conserved Domains (1) summary
      pfam12530
      Location:528 → 752
      DUF3730; Protein of unknown function (DUF3730)

    5. XM_036164000.1 → XP_036019893.1  focadhesin isoform X6

      Conserved Domains (2) summary
      pfam11229
      Location:1248 → 1412
      Focadhesin
      pfam12530
      Location:528 → 752
      DUF3730; Protein of unknown function (DUF3730)

    6. XM_036163997.1 → XP_036019890.1  focadhesin isoform X2

      Conserved Domains (2) summary
      pfam11229
      Location:1162 → 1750
      Focadhesin
      pfam12530
      Location:442 → 666
      DUF3730; Protein of unknown function (DUF3730)

    7. XM_036163996.1 → XP_036019889.1  focadhesin isoform X1

      Conserved Domains (2) summary
      pfam11229
      Location:1248 → 1836
      Focadhesin
      pfam12530
      Location:528 → 752
      DUF3730; Protein of unknown function (DUF3730)

    8. XM_036163998.1 → XP_036019891.1  focadhesin isoform X3

      Conserved Domains (2) summary
      pfam11229
      Location:1127 → 1715
      Focadhesin
      pfam12530
      Location:407 → 631
      DUF3730; Protein of unknown function (DUF3730)

    9. XM_006537884.4 → XP_006537947.1  focadhesin isoform X5

      Conserved Domains (2) summary
      pfam11229
      Location:1113 → 1701
      Focadhesin
      pfam12530
      Location:393 → 617
      DUF3730; Protein of unknown function (DUF3730)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2AKG8.1 GenPept UniProtKB/Swiss-Prot:A2AKG8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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