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    TTC39C tetratricopeptide repeat domain 39C [ Homo sapiens (human) ]

    Gene ID: 125488, updated on 9-Dec-2024

    Summary

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    Official Symbol
    TTC39Cprovided by HGNC
    Official Full Name
    tetratricopeptide repeat domain 39Cprovided by HGNC
    Primary source
    HGNC:HGNC:26595
    See related
    Ensembl:ENSG00000168234 AllianceGenome:HGNC:26595
    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
    HsT2697; C18orf17
    Summary
    Predicted to be involved in cilium assembly and otolith morphogenesis. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in liver (RPKM 7.1), skin (RPKM 3.6) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TTC39C in Genome Data Viewer
    Location:
    18q11.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (23992887..24135600)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (24187146..24329927)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (21572851..21715564)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21299932-21300432 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21300433-21300933 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:21305921-21306891 Neighboring gene ribosomal protein L23a pseudogene 77 Neighboring gene laminin subunit alpha 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:21427116-21427961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13165 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:21452354-21453553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:21531393-21532253 Neighboring gene MPRA-validated peak3071 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13166 Neighboring gene long intergenic non-protein coding RNA 2958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9362 Neighboring gene TTC39C antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13170 Neighboring gene Sharpr-MPRA regulatory region 15364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13171 Neighboring gene RNA, U5A small nuclear 6, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 452 Neighboring gene calcium binding tyrosine phosphorylation regulated Neighboring gene oxysterol binding protein like 1A

    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. Ttc39c is a potential target for the treatment of lung cancer. Rong H, et al. BMC Pulm Med, 2022 Oct 27. PMID 36303158, Free PMC Article
    2. A genome-wide association study implicates that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity. Meng W, et al. Ophthalmic Genet, 2019 Jun. PMID 31264924
    3. DNA sequence and analysis of human chromosome 18. Nusbaum C, et al. Nature, 2005 Sep 22. PMID 16177791
    4. The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets. Katsogiannou M, et al. Mol Cell Proteomics, 2014 Dec. PMID 25277244, Free PMC Article
    5. Elucidation of the BMI1 interactome identifies novel regulatory roles in glioblastoma. Freire-Benéitez V, et al. NAR Cancer, 2021 Mar. PMID 34316702, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ttc39c is a potential target for the treatment of lung cancer.
      Title: Ttc39c is a potential target for the treatment of lung cancer.
    2. Single Nucleotide Polymorphism in the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity.
      Title: A genome-wide association study implicates that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ33761, FLJ90394

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in otolith morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    tetratricopeptide repeat protein 39C
    Names
    TPR repeat protein 39C

    NCBI Reference Sequences (RefSeq)

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    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_001135993.2 → NP_001129465.1  tetratricopeptide repeat protein 39C isoform 1

      See identical proteins and their annotated locations for NP_001129465.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC010754, AC090772, KF456356
      Consensus CDS
      CCDS45839.1
      UniProtKB/Swiss-Prot
      B7WP63, J3QRR1, Q0VAJ2, Q8N284, Q8N584
      Related
      ENSP00000323645.3, ENST00000317571.8
      Conserved Domains (1) summary
      pfam10300
      Location:34 → 498
      DUF3808; Protein of unknown function (DUF3808)

    2. NM_001243425.2 → NP_001230354.1  tetratricopeptide repeat protein 39C isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and lacks a large portion of the 3' coding region, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC016833
      Consensus CDS
      CCDS58616.1
      UniProtKB/Swiss-Prot
      Q8N584
      Related
      ENSP00000464344.1, ENST00000584250.2
      Conserved Domains (1) summary
      pfam10300
      Location:34 → 58
      DUF3808; Protein of unknown function (DUF3808)

    3. NM_001292030.2 → NP_001278959.1  tetratricopeptide repeat protein 39C isoform 4 precursor

      See identical proteins and their annotated locations for NP_001278959.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks part of the 5' coding region, contains an alternate 5'-terminal exon, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC090772, KF456356
      Consensus CDS
      CCDS77165.1
      UniProtKB/TrEMBL
      B7Z3X0, G3V1P2
      Related
      ENSP00000443016.1, ENST00000540918.3
      Conserved Domains (1) summary
      pfam10300
      Location:11 → 191
      DUF3808; Protein of unknown function (DUF3808)

    4. NM_153211.4 → NP_694943.2  tetratricopeptide repeat protein 39C isoform 2

      See identical proteins and their annotated locations for NP_694943.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR, lacks an in-frame portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC010754, AC090772, KF456356
      Consensus CDS
      CCDS32804.1
      UniProtKB/Swiss-Prot
      Q8N584
      Related
      ENSP00000306598.6, ENST00000304621.10
      Conserved Domains (1) summary
      pfam10300
      Location:1 → 437
      DUF3808; Protein of unknown function (DUF3808)

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      23992887..24135600
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437297.1 → XP_047293253.1  tetratricopeptide repeat protein 39C isoform X3

    2. XM_047437298.1 → XP_047293254.1  tetratricopeptide repeat protein 39C isoform X3

    3. XM_047437296.1 → XP_047293252.1  tetratricopeptide repeat protein 39C isoform X1

    4. XM_011525814.4 → XP_011524116.1  tetratricopeptide repeat protein 39C isoform X2

      Conserved Domains (1) summary
      pfam10300
      Location:34 → 462
      DUF3808; Protein of unknown function (DUF3808)

    5. XM_006722392.4 → XP_006722455.1  tetratricopeptide repeat protein 39C isoform X4

      Conserved Domains (1) summary
      pfam10300
      Location:34 → 329
      DUF3808; Protein of unknown function (DUF3808)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      24187146..24329927
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318197.1 → XP_054174172.1  tetratricopeptide repeat protein 39C isoform X3

    2. XM_054318198.1 → XP_054174173.1  tetratricopeptide repeat protein 39C isoform X3

    3. XM_054318195.1 → XP_054174170.1  tetratricopeptide repeat protein 39C isoform X1

    4. XM_054318196.1 → XP_054174171.1  tetratricopeptide repeat protein 39C isoform X2

    5. XM_054318199.1 → XP_054174174.1  tetratricopeptide repeat protein 39C isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N584.2 GenPept UniProtKB/Swiss-Prot:Q8N584

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