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

Gene ID: 134121, updated on 11-Apr-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
Located in ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis (RPKM 8.1), lung (RPKM 2.5) and 5 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (7830378..7851133, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (7769514..7790256, complement)
105.20220307 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
  • 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 
Component Evidence Code Pubs
located_in axonemal B tubule inner sheath IEA
Inferred from Electronic Annotation
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 

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_2023_10

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

Gene LinkOut

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

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