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    FLACC1 flagellum associated containing coiled-coil domains 1 [ Homo sapiens (human) ]

    Gene ID: 130540, updated on 2-Nov-2024

    Summary

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    Official Symbol
    FLACC1provided by HGNC
    Official Full Name
    flagellum associated containing coiled-coil domains 1provided by HGNC
    Primary source
    HGNC:HGNC:14439
    See related
    Ensembl:ENSG00000155749 MIM:619796; AllianceGenome:HGNC:14439
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALS2CR12
    Summary
    Predicted to be located in cytoplasmic vesicle and outer dense fiber. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 8.4), lung (RPKM 1.1) and 3 other tissues See more
    Orthologs
    all
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    Genomic context

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    See FLACC1 in Genome Data Viewer
    Location:
    2q33.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (201288271..201364289, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (201768929..201844975, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (202152994..202222068, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene caspase 10 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:202084159-202084703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16982 Neighboring gene MT-ND4L pseudogene 13 Neighboring gene MT-ND4 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16986 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:202122995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16989 Neighboring gene caspase 8 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 2:202153225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202184683-202185184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202185185-202185684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16990 Neighboring gene trafficking kinesin protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202289002-202289502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:202289503-202290003 Neighboring gene SCYL2 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:202315536-202316390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12232 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:202329405-202329904 Neighboring gene STE20 related adaptor beta

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Expression of a sperm flagellum component encoded by the Als2cr12 gene. Choi E, et al. Gene Expr Patterns, 2011 Jun-Jul. PMID 21402173
    2. Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk. Lin WY, et al. Hum Mol Genet, 2015 Jan 1. PMID 25168388, Free PMC Article
    3. New basal cell carcinoma susceptibility loci. Stacey SN, et al. Nat Commun, 2015 Apr 9. PMID 25855136, Free PMC Article
    4. Genome-wide association study identifies three new melanoma susceptibility loci. Barrett JH, et al. Nat Genet, 2011 Oct 9. PMID 21983787, Free PMC Article
    5. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. Wu C, et al. Nat Genet, 2014 Sep. PMID 25129146, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. rs13014235 is associated with susceptibility to cutaneous basal cell carcinoma.
      Title: New basal cell carcinoma susceptibility loci.
    2. Genome-wide association studies show a significant association between the intronic SNP rs1830298 in ALS2CR12 gene and breast cancer; further expression studies suggest that CASP8 might be the target gene.
      Title: Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk.
    3. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association study identifies three new melanoma susceptibility loci.
    EBI GWAS Catalog
    Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in outer dense fiber ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in sperm flagellum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    flagellum-associated coiled-coil domain-containing protein 1
    Names
    ALS2 chromosome region 12
    amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12
    amyotrophic lateral sclerosis 2 chromosomal region candidate gene 12 protein
    amyotrophic lateral sclerosis 2 chromosome region 12
    amyotrophic lateral sclerosis 2 chromosome region candidate 12

    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_001127391.3 → NP_001120863.1  flagellum-associated coiled-coil domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001120863.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 encode the same protein (isoform b).
      Source sequence(s)
      AB053314, BC031603, BX095441, DB034999
      Consensus CDS
      CCDS46488.1
      UniProtKB/TrEMBL
      A8K8B8
      Related
      ENSP00000376086.3, ENST00000392257.8
      Conserved Domains (1) summary
      TIGR02168
      Location:113 → 393
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    2. NM_001289993.2 → NP_001276922.1  flagellum-associated coiled-coil domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001276922.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 encode the same protein (isoform b).
      Source sequence(s)
      AB053314, AC007256, AK292283
      Consensus CDS
      CCDS46488.1
      UniProtKB/TrEMBL
      A8K8B8
      Related
      ENSP00000412073.1, ENST00000439709.5
      Conserved Domains (1) summary
      TIGR02168
      Location:113 → 393
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    3. NM_139163.4 → NP_631902.2  flagellum-associated coiled-coil domain-containing protein 1 isoform a

      See identical proteins and their annotated locations for NP_631902.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AB053314, AC007256, CD703925, DB054409
      Consensus CDS
      CCDS2346.1
      UniProtKB/Swiss-Prot
      G5E9S3, Q53TT6, Q8N1B6, Q96Q35
      UniProtKB/TrEMBL
      A8K8B8
      Related
      ENSP00000385098.2, ENST00000405148.6
      Conserved Domains (1) summary
      TIGR02169
      Location:117 → 399
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    RNA

    1. NR_110620.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB053314, AC007256, AK124115, CD703925, DB054409
      Related
      ENST00000494171.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      201288271..201364289 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024452696.2 → XP_024308464.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      G5E9S3, Q53TT6, Q8N1B6, Q96Q35
      UniProtKB/TrEMBL
      A8K8B8
      Conserved Domains (1) summary
      TIGR02169
      Location:117 → 399
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    2. XM_047443393.1 → XP_047299349.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X3

    3. XM_011510606.4 → XP_011508908.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A8K8B8
      Conserved Domains (1) summary
      TIGR02168
      Location:127 → 361
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    4. XM_047443395.1 → XP_047299351.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

    5. XM_047443394.1 → XP_047299350.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

    6. XM_011510610.4 → XP_011508912.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X5

    7. XM_011510612.4 → XP_011508914.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X7

    8. XM_047443396.1 → XP_047299352.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      201768929..201844975 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340534.1 → XP_054196509.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X1

    2. XM_054340536.1 → XP_054196511.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X3

    3. XM_054340535.1 → XP_054196510.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X2

    4. XM_054340538.1 → XP_054196513.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

    5. XM_054340537.1 → XP_054196512.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X4

    6. XM_054340539.1 → XP_054196514.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X5

    7. XM_054340541.1 → XP_054196516.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X7

    8. XM_054340540.1 → XP_054196515.1  flagellum-associated coiled-coil domain-containing protein 1 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96Q35.2 GenPept UniProtKB/Swiss-Prot:Q96Q35

    Gene LinkOut

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

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