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Focad focadhesin [ Mus musculus (house mouse) ]

Gene ID: 230393, updated on 5-Mar-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 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
human all
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Genomic context

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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 (17) 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 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
  

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

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