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    CFAP90 cilia and flagella associated protein 90 [ Homo sapiens (human) ]

    Gene ID: 134121, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CFAP90provided by HGNC
    Official Full Name
    cilia and flagella associated protein 90provided by HGNC
    Primary source
    HGNC:HGNC:27028
    See related
    Ensembl:ENSG00000215217 AllianceGenome:HGNC:27028
    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
    C5orf49
    Summary
    Predicted to be involved in flagellated sperm motility. Located in axoneme and ciliary basal body. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 8.1), lung (RPKM 2.5) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CFAP90 in Genome Data Viewer
    Location:
    5p15.31
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (7830378..7851133, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (7769514..7790256, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (7830491..7851246, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7394801-7395566 Neighboring gene long intergenic non-protein coding RNA 2142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7395567-7396332 Neighboring gene uncharacterized LOC105374646 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7420020-7420743 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7420744-7421468 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:7422307-7423176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7424665-7425194 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7425195-7425722 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:7427184-7427875 Neighboring gene adenylate cyclase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7480982-7481482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7481483-7481983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7515349-7515849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7526205-7526704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7596934-7597448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7597449-7597963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7663263-7663836 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:7663837-7664409 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:7667125-7668324 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:7683613-7683799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22346 Neighboring gene Sharpr-MPRA regulatory region 1766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7815313-7815850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7816087-7816815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7816816-7817543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15905 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15906 Neighboring gene FAST kinase domains 3 Neighboring gene uncharacterized LOC124900936 Neighboring gene 5-methyltetrahydrofolate-homocysteine methyltransferase reductase

    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. Genomic analysis of Meckel-Gruber syndrome in Arabs reveals marked genetic heterogeneity and novel candidate genes. Shaheen R, et al. Eur J Hum Genet, 2013 Jul. PMID 23169490, Free PMC Article
    2. Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. Sigg MA, et al. Dev Cell, 2017 Dec 18. PMID 29257953, Free PMC Article
    3. SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules. Gui M, et al. Proc Natl Acad Sci U S A, 2022 Oct 11. PMID 36191189, Free PMC Article
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    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

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in flagellated sperm motility ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axonemal B tubule inner sheath ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in axoneme IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in sperm flagellum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    cilia- and flagella-associated protein 90
    Names
    uncharacterized protein C5orf49

    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_001089584.3 → NP_001083053.1  cilia- and flagella-associated protein 90

      See identical proteins and their annotated locations for NP_001083053.1

      Status: VALIDATED

      Source sequence(s)
      AC010346, BC062569
      Consensus CDS
      CCDS43300.1
      UniProtKB/Swiss-Prot
      A4QMS7
      UniProtKB/TrEMBL
      D6RHK3
      Related
      ENSP00000382708.2, ENST00000399810.7
      Conserved Domains (1) summary
      pfam15074
      Location:42 → 131
      DUF4541; Domain of unknown function (DUF4541)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      7830378..7851133 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011513963.3 → XP_011512265.1  cilia- and flagella-associated protein 90 isoform X1

      Conserved Domains (1) summary
      pfam15074
      Location:18 → 99
      DUF4541; Domain of unknown function (DUF4541)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      7769514..7790256 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351610.1 → XP_054207585.1  cilia- and flagella-associated protein 90 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A4QMS7.1 GenPept UniProtKB/Swiss-Prot:A4QMS7

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