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    Focad focadhesin [ Mus musculus (house mouse) ]

    Gene ID: 230393, updated on 1-Mar-2024

    Summary

    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 located in focal adhesion. Is expressed in diencephalon lateral wall ventricular layer and midbrain ventricular layer. Orthologous to human FOCAD (focadhesin). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in frontal lobe adult (RPKM 3.5), cortex adult (RPKM 3.3) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    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

    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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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 anchoring junction IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in focal adhesion ISO
    Inferred from Sequence Orthology
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001081184.2NP_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:12101798
      DUF3028; Protein of unknown function (DUF3028)
      pfam12530
      Location:490714
      DUF3730; Protein of unknown function (DUF3730)
    2. NM_001419409.1NP_001406338.1  focadhesin isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL772316, AL831756, BX572638
      UniProtKB/TrEMBL
      E9PYJ6
      Related
      ENSMUSP00000124298.2, ENSMUST00000159342.8
    3. NM_001419410.1NP_001406339.1  focadhesin isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL772316, AL831756, BX572638
    4. NM_001419411.1NP_001406340.1  focadhesin isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL772296, AL831756
    5. NM_001419412.1NP_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_030253421.2XP_030109281.1  focadhesin isoform X3

      Conserved Domains (2) summary
      pfam11229
      Location:11271715
      Focadhesin
      pfam12530
      Location:407631
      DUF3730; Protein of unknown function (DUF3730)
    2. XM_036164001.1XP_036019894.1  focadhesin isoform X8

      Conserved Domains (1) summary
      pfam12530
      Location:528752
      DUF3730; Protein of unknown function (DUF3730)
    3. XM_006537886.4XP_006537949.1  focadhesin isoform X9

      Conserved Domains (1) summary
      pfam12530
      Location:528752
      DUF3730; Protein of unknown function (DUF3730)
    4. XM_006537885.5XP_006537948.1  focadhesin isoform X7

      Conserved Domains (1) summary
      pfam12530
      Location:528752
      DUF3730; Protein of unknown function (DUF3730)
    5. XM_036164000.1XP_036019893.1  focadhesin isoform X6

      Conserved Domains (2) summary
      pfam11229
      Location:12481412
      Focadhesin
      pfam12530
      Location:528752
      DUF3730; Protein of unknown function (DUF3730)
    6. XM_036163997.1XP_036019890.1  focadhesin isoform X2

      Conserved Domains (2) summary
      pfam11229
      Location:11621750
      Focadhesin
      pfam12530
      Location:442666
      DUF3730; Protein of unknown function (DUF3730)
    7. XM_036163996.1XP_036019889.1  focadhesin isoform X1

      Conserved Domains (2) summary
      pfam11229
      Location:12481836
      Focadhesin
      pfam12530
      Location:528752
      DUF3730; Protein of unknown function (DUF3730)
    8. XM_036163998.1XP_036019891.1  focadhesin isoform X3

      Conserved Domains (2) summary
      pfam11229
      Location:11271715
      Focadhesin
      pfam12530
      Location:407631
      DUF3730; Protein of unknown function (DUF3730)
    9. XM_006537884.4XP_006537947.1  focadhesin isoform X5

      Conserved Domains (2) summary
      pfam11229
      Location:11131701
      Focadhesin
      pfam12530
      Location:393617
      DUF3730; Protein of unknown function (DUF3730)