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FOCAD focadhesin [ Homo sapiens (human) ]

Gene ID: 54914, updated on 22-Sep-2022

Summary

Official Symbol
FOCADprovided by HGNC
Official Full Name
focadhesinprovided by HGNC
Primary source
HGNC:HGNC:23377
See related
Ensembl:ENSG00000188352 MIM:614606; AllianceGenome:HGNC:23377
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
SCOLIV; KIAA1797
Summary
Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]
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:
49
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (20655625..20995950)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (20672105..21009826)
105.20220307 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 microRNA 4474 Neighboring gene ribosomal protein L7a pseudogene 48 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

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
Liver disease, severe congenital
MedGen: CN315947 OMIM: 619991 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
EBI GWAS Catalog

Pathways from PubChem

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 
Process Evidence Code Pubs
involved_in regulation of post-transcriptional gene silencing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
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_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
    UniProtKB/Swiss-Prot
    Q9NX87
    Related
    ENSP00000344307.6, ENST00000338382.11
    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, Q9NX87
    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 Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    20655625..20995950
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423537.1XP_047279493.1  focadhesin isoform X9

    UniProtKB/Swiss-Prot
    Q9NX87
  2. XM_047423539.1XP_047279495.1  focadhesin isoform X10

  3. XM_017014855.2XP_016870344.1  focadhesin isoform X5

  4. XM_047423532.1XP_047279488.1  focadhesin isoform X3

  5. XM_047423535.1XP_047279491.1  focadhesin isoform X7

  6. XM_047423534.1XP_047279490.1  focadhesin isoform X6

  7. XM_017014852.2XP_016870341.2  focadhesin isoform X1

  8. XM_047423533.1XP_047279489.1  focadhesin isoform X4

  9. XM_047423536.1XP_047279492.1  focadhesin isoform X8

  10. XM_047423531.1XP_047279487.1  focadhesin isoform X2

  11. XM_047423538.1XP_047279494.1  focadhesin isoform X9

    UniProtKB/Swiss-Prot
    Q9NX87
  12. XM_017014856.2XP_016870345.1  focadhesin isoform X5

  13. XM_047423540.1XP_047279496.1  focadhesin isoform X11

  14. XM_024447586.2XP_024303354.1  focadhesin isoform X12

    Conserved Domains (2) summary
    pfam11229
    Location:11081696
    Focadhesin
    pfam12530
    Location:385609
    DUF3730; Protein of unknown function (DUF3730)
  15. XM_017014859.2XP_016870348.1  focadhesin isoform X13

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    20672105..21009826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)