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FOCAD focadhesin [ Homo sapiens (human) ]

Gene ID: 54914, updated on 11-Jun-2021

Summary

Official Symbol
FOCADprovided by HGNC
Official Full Name
focadhesinprovided by HGNC
Primary source
HGNC:HGNC:23377
See related
Ensembl:ENSG00000188352 MIM:614606
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KIAA1797
Expression
Ubiquitous expression in thyroid (RPKM 11.9), adrenal (RPKM 7.1) and 25 other tissues See more
Orthologs
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Genomic context

See FOCAD in Genome Data Viewer
Location:
9p21.3
Exon count:
50
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (20658309..20995953)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (20658308..20995949)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MLLT3 super elongation complex subunit Neighboring gene ribosomal protein L7a pseudogene 48 Neighboring gene uncharacterized LOC107987052 Neighboring gene FOCAD antisense RNA 1 Neighboring gene microRNA 491 Neighboring gene small nucleolar RNA, H/ACA box 30B Neighboring gene uncharacterized LOC105375989 Neighboring gene 3-hydroxyacyl-CoA dehydratase 4 Neighboring gene interferon nu 1, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20375, KIAA1797

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

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_001375567.1NP_001362496.1  focadhesin isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AL354879, AL392163, AL445624, AL662879, KF458909
    Related
    ENSP00000344307.6, ENST00000338382.10
    Conserved Domains (2) summary
    pfam11229
    Location:12131801
    Focadhesin
    pfam12530
    Location:490714
    DUF3730; Protein of unknown function (DUF3730)
  2. NM_001375568.1NP_001362497.1  focadhesin isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame coding exon in the mid-coding region compared to variant 1, resulting in a shorter isoform (2) lacking an internal protein segment compared to isoform 1. Note, while isoforms 2 and 3 are the same length (1766 aa), they lack different protein segments compared to isoform 1.
    Source sequence(s)
    AL354879, AL392163, AL445624, AL662879, KF458909
    Conserved Domains (2) summary
    pfam11229
    Location:11781766
    Focadhesin
    pfam12530
    Location:453679
    DUF3730; Protein of unknown function (DUF3730)
  3. NM_001375570.1NP_001362499.1  focadhesin isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame coding exon in the 5'-coding region compared to variant 1, resulting in a shorter isoform (3) lacking an internal protein segment compared to isoform 1. Note, while isoforms 2 and 3 are the same length (1766 aa), they lack different protein segments compared to isoform 1.
    Source sequence(s)
    AL354879, AL392163, AL445624, AL662879, KF458909
    Conserved Domains (2) summary
    pfam11229
    Location:11781766
    Focadhesin
    pfam12530
    Location:455679
    DUF3730; Protein of unknown function (DUF3730)
  4. NM_017794.5NP_060264.4  focadhesin isoform 1

    See identical proteins and their annotated locations for NP_060264.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AK055116, AK056522, AL445624, AY139834
    Consensus CDS
    CCDS34993.1
    UniProtKB/Swiss-Prot
    Q5VW36
    UniProtKB/TrEMBL
    B3KNV9
    Related
    ENSP00000369599.1, ENST00000380249.5
    Conserved Domains (2) summary
    pfam11229
    Location:12131801
    Focadhesin
    pfam12530
    Location:490714
    DUF3730; Protein of unknown function (DUF3730)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    20658309..20995953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014855.1XP_016870344.1  focadhesin isoform X1

  2. XM_017014856.1XP_016870345.1  focadhesin isoform X1

  3. XM_017014852.1XP_016870341.1  focadhesin isoform X1

  4. XM_017014853.1XP_016870342.1  focadhesin isoform X2

  5. XM_017014854.1XP_016870343.1  focadhesin isoform X3

  6. XM_024447585.1XP_024303353.1  focadhesin isoform X4

    Conserved Domains (2) summary
    pfam11229
    Location:11781766
    Focadhesin
    pfam12530
    Location:453679
    DUF3730; Protein of unknown function (DUF3730)
  7. XM_011517945.2XP_011516247.1  focadhesin isoform X5

    Conserved Domains (2) summary
    pfam11229
    Location:11781766
    Focadhesin
    pfam12530
    Location:455679
    DUF3730; Protein of unknown function (DUF3730)
  8. XM_024447586.1XP_024303354.1  focadhesin isoform X7

    Conserved Domains (2) summary
    pfam11229
    Location:11081696
    Focadhesin
    pfam12530
    Location:385609
    DUF3730; Protein of unknown function (DUF3730)
  9. XM_017014859.1XP_016870348.1  focadhesin isoform X8

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