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    DLEC1 DLEC1 cilia and flagella associated protein [ Homo sapiens (human) ]

    Gene ID: 9940, updated on 27-Nov-2024

    Summary

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    Official Symbol
    DLEC1provided by HGNC
    Official Full Name
    DLEC1 cilia and flagella associated proteinprovided by HGNC
    Primary source
    HGNC:HGNC:2899
    See related
    Ensembl:ENSG00000008226 MIM:604050; AllianceGenome:HGNC:2899
    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
    F56; DLC1; DLC-1; FAP81; CFAP81
    Summary
    The cytogenetic location of this gene is 3p21.3, and it is located in a region that is commonly deleted in a variety of malignancies. Down-regulation of this gene has been observed in several human cancers including lung, esophageal, renal tumors, and head and neck squamous cell carcinoma. In some cases, reduced expression of this gene in tumor cells is a result of aberrant promoter methylation. Several alternatively spliced transcripts have been observed that contain disrupted coding regions and likely encode nonfunctional proteins.[provided by RefSeq, Mar 2016]
    Expression
    Biased expression in testis (RPKM 8.8), lung (RPKM 3.8) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DLEC1 in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38039208..38124025)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38043402..38129694)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38080699..38165516)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12639 Neighboring gene Sharpr-MPRA regulatory region 7921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38035775-38036392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38039104-38039674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38047479-38047979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38050723-38051473 Neighboring gene villin like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14204 Neighboring gene phospholipase C delta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38094034-38094878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19678 Neighboring gene protein phosphatase 2 regulatory subunit Bdelta pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:38124731-38125295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38139347-38139846 Neighboring gene uncharacterized LOC105377033 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38152870-38153688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38158759-38159717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38179733-38180676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19681 Neighboring gene acetyl-CoA acyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38196601-38197102 Neighboring gene uncharacterized LOC101928234 Neighboring gene MYD88 innate immune signal transduction adaptor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38205703-38206902 Neighboring gene oxidative stress responsive kinase 1

    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. Candidate tumor-suppressor gene DLEC1 is frequently downregulated by promoter hypermethylation and histone hypoacetylation in human epithelial ovarian cancer. Kwong J, et al. Neoplasia, 2006 Apr. PMID 16756719, Free PMC Article
    2. Frequent epigenetic inactivation of deleted in lung and esophageal cancer 1 gene by promoter methylation in non-small-cell lung cancer. Zhang Y, et al. Clin Lung Cancer, 2010 Jul 1. PMID 20630829
    3. Aberrant promoter methylation of DLEC1, a critical 3p22 tumor suppressor for renal cell carcinoma, is associated with more advanced tumor stage. Zhang Q, et al. J Urol, 2010 Aug. PMID 20639048
    4. Transcriptional repression of DLEC1 associates with the depth of tumor invasion in oral squamous cell carcinoma. Chan WH, et al. Oral Oncol, 2010 Dec. PMID 20952247
    5. Epigenetic inactivation of deleted in lung and esophageal cancer 1 gene by promoter methylation in gastric and colorectal adenocarcinoma. Zhang Y, et al. Hepatogastroenterology, 2010 Nov-Dec. PMID 21443130

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dlec1 is required for spermatogenesis and male fertility in mice.
      Title: Dlec1 is required for spermatogenesis and male fertility in mice.
    2. PM2.5 exposure and DLEC1 promoter methylation in Taiwan Biobank participants.
      Title: PM(2.5) exposure and DLEC1 promoter methylation in Taiwan Biobank participants.
    3. Compared with negative methylation (Nm), DLEC1-positive methylation (Pm) was associated with increased GC risk in PS (OR 2.083, 95% CI 1.220-3.558, P = 0.007), but PBX3 Pm was not associated with GC risk.
      Title: Relationship between DLEC1 and PBX3 promoter methylation and the risk and prognosis of gastric cancer in peripheral blood leukocytes.
    4. that the KLF4 and DLEC1 genes can be considered potential methylation biomarkers for uterine leiomyomas
      Title: Different methylation levels in the KLF4, ATF3 and DLEC1 genes in the myometrium and in corpus uteri mesenchymal tumours as assessed by MS-HRM.
    5. DLEC1 methylation can be utilized to identify a subset with a better prognosis in intrahepatic cholangiocarcinomas of the small duct type.
      Title: DLEC1 methylation is associated with a better clinical outcome in patients with intrahepatic cholangiocarcinoma of the small duct subtype.
    6. We found no correlation between the DLEC1, TUSC4 and MLH1 gene expression and NSCLC patient characteristics (gender, age and smoking) or cancer histopathology. No significant differences in the gene expression among NSCLC subtypes indicate the weakness of DLEC1, TUSC4 and MLH1 expression analysis as potential differentiating markers of NSCLC subtypes in the Polish population.
      Title: Small suitability of the DLEC1, MLH1 and TUSC4 mRNA expression analysis as potential prognostic or differentiating markers for NSCLC patients in the Polish population.
    7. the expression levels of DLEC1 and ITGA9 were prominently decreased in lung tumor samples
      Title: Expression level and methylation status of three tumor suppressor genes, DLEC1, ITGA9 and MLH1, in non-small cell lung cancer.
    8. DLEC1 mediates tumor-suppressive activities through NF-kappaB signaling.
      Title: DLEC1, a 3p tumor suppressor, represses NF-κB signaling and is methylated in prostate cancer.
    9. DLEC1 methylation was not associated with the clinicopathological variables of gastric cancer.
      Title: Methylation of DLEC1 promoter is a predictor for recurrence in Chinese patients with gastric cancer.
    10. DLEC1 is down-regulated in head and neck squamous cell tumors and it's promoter methylation is not associated with the clinicopathological parameters.
      Title: DLEC1 is not silenced solely by promoter methylation in head and neck squamous cell carcinoma.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables alpha-tubulin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables beta-tubulin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tubulin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to tumor cell IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    deleted in lung and esophageal cancer protein 1
    Names
    DLEC, cilia and flagella associated protein
    cilia and flagella associated protein 81
    deleted in lung and esophageal cancer 1

    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.

    Genomic

    1. NG_023237.1 RefSeqGene

      Range
      5004..89821
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001321153.2 → NP_001308082.1  deleted in lung and esophageal cancer protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AB020522, AB425198, AP006309, CB243860
      UniProtKB/TrEMBL
      B1B5Y4

    2. NM_007335.4 → NP_031361.2  deleted in lung and esophageal cancer protein 1 isoform DLEC1-N1

      See identical proteins and their annotated locations for NP_031361.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (DLEC1-N1) encodes the shortest isoform.
      Source sequence(s)
      AB020522, AL137706, AP006309, CB243860
      Consensus CDS
      CCDS2672.2
      UniProtKB/Swiss-Prot
      Q9NSW0, Q9NTG5, Q9Y238
      UniProtKB/TrEMBL
      B7ZW06
      Related
      ENSP00000308597.6, ENST00000308059.11

    3. NM_007337.4 → NP_031363.2  deleted in lung and esophageal cancer protein 1 isoform DLEC1-S3

      See identical proteins and their annotated locations for NP_031363.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (DLEC1-S3) lacks an exon in the 3' coding region that results in a frameshift and use of a downstream stop codon, compared to variant DLEC1-N1. The encoded isoform (DLEC1-S3) has a longer, distinct C-terminus compared to the DLEC1-N1 isoform. There are currently no publicly available full-length transcripts supporting this variant, but it is supported by data in PMID:10213508.
      Source sequence(s)
      AB020522, AL137706, AP006309, CB243860
      UniProtKB/TrEMBL
      B7ZW06
      Related
      ENSP00000315914.5, ENST00000346219.7

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      38039208..38124025
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534317.3 → XP_011532619.1  deleted in lung and esophageal cancer protein 1 isoform X1

      UniProtKB/TrEMBL
      B1B5Y4

    2. XM_006713438.4 → XP_006713501.1  deleted in lung and esophageal cancer protein 1 isoform X2

      UniProtKB/TrEMBL
      B1B5Y4

    3. XM_011534318.3 → XP_011532620.1  deleted in lung and esophageal cancer protein 1 isoform X3

      UniProtKB/TrEMBL
      B1B5Y4

    4. XM_006713439.4 → XP_006713502.1  deleted in lung and esophageal cancer protein 1 isoform X4

      UniProtKB/TrEMBL
      B1B5Y4

    5. XM_006713440.4 → XP_006713503.1  deleted in lung and esophageal cancer protein 1 isoform X5

      UniProtKB/TrEMBL
      B1B5Y4

    6. XM_047449369.1 → XP_047305325.1  deleted in lung and esophageal cancer protein 1 isoform X6

    7. XM_047449370.1 → XP_047305326.1  deleted in lung and esophageal cancer protein 1 isoform X7

    RNA

    1. XR_940527.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      38043402..38129694
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348647.1 → XP_054204622.1  deleted in lung and esophageal cancer protein 1 isoform X1

    2. XM_054348648.1 → XP_054204623.1  deleted in lung and esophageal cancer protein 1 isoform X2

    3. XM_054348649.1 → XP_054204624.1  deleted in lung and esophageal cancer protein 1 isoform X3

    4. XM_054348650.1 → XP_054204625.1  deleted in lung and esophageal cancer protein 1 isoform X4

    5. XM_054348651.1 → XP_054204626.1  deleted in lung and esophageal cancer protein 1 isoform X5

    6. XM_054348652.1 → XP_054204627.1  deleted in lung and esophageal cancer protein 1 isoform X6

    7. XM_054348653.1 → XP_054204628.1  deleted in lung and esophageal cancer protein 1 isoform X7

    RNA

    1. XR_008486873.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_007336.1: Suppressed sequence

      Description
      NM_007336.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_007338.2: Suppressed sequence

      Description
      NM_007338.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y238.2 GenPept UniProtKB/Swiss-Prot:Q9Y238

    Gene LinkOut

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

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