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    RTEL1 regulator of telomere elongation helicase 1 [ Homo sapiens (human) ]

    Gene ID: 51750, updated on 13-May-2024

    Summary

    Official Symbol
    RTEL1provided by HGNC
    Official Full Name
    regulator of telomere elongation helicase 1provided by HGNC
    Primary source
    HGNC:HGNC:15888
    See related
    Ensembl:ENSG00000258366 MIM:608833; AllianceGenome:HGNC:15888
    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
    NHL; RTEL; DKCA4; DKCB5; PFBMFT3; C20orf41
    Summary
    This gene encodes a DNA helicase which functions in the stability, protection and elongation of telomeres and interacts with proteins in the shelterin complex known to protect telomeres during DNA replication. Mutations in this gene have been associated with dyskeratosis congenita and Hoyerall-Hreidarsson syndrome. Read-through transcription of this gene into the neighboring downstream gene, which encodes tumor necrosis factor receptor superfamily, member 6b, generates a non-coding transcript. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
    Expression
    Ubiquitous expression in testis (RPKM 6.4), appendix (RPKM 4.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RTEL1 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63657810..63696253)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65471931..65516559)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62289163..62327606)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13168 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18236 Neighboring gene melanoma highly expressed competing endogenous lncRNA for miR-425 and miR-489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62269990-62270750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62272271-62273029 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62273358-62274096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62275446-62276015 Neighboring gene Sharpr-MPRA regulatory region 12780 Neighboring gene stathmin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62282910-62283480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62284757-62285436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62285437-62286115 Neighboring gene RTEL1-TNFRSF6B readthrough (NMD candidate) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18241 Neighboring gene uncharacterized LOC124904954 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62320674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62330893-62331773 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13178 Neighboring gene ADP ribosylation factor related protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62339316-62340276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62347847-62348348 Neighboring gene zinc finger CCCH-type and G-patch domain containing Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:62359961-62360460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363158-62363701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363702-62364244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18250 Neighboring gene Lck interacting transmembrane adaptor 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Chromosome 7p11.2 (EGFR) variation influences glioma risk.
    EBI GWAS Catalog
    Genome-wide association scan of dental caries in the permanent dentition.
    EBI GWAS Catalog
    Genome-wide association study identifies five susceptibility loci for glioma.
    EBI GWAS Catalog
    Genome-wide association study of glioma and meta-analysis.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog
    Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility.
    EBI GWAS Catalog
    Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1088, bK3184A7.3, DKFZp434C013

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ATP binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA helicase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA helicase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables DNA helicase activity TAS
    Traceable Author Statement
    more info
     
    enables DNA polymerase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in DNA duplex unwinding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA strand displacement ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DNA strand displacement TAS
    Traceable Author Statement
    more info
     
    involved_in mitotic telomere maintenance via semi-conservative replication ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of DNA recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of DNA recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of t-circle formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of t-circle formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of t-circle formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in negative regulation of t-circle formation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of telomere maintenance in response to DNA damage ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of telomere capping IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of telomere maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of telomere maintenance via telomere lengthening IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of telomeric loop disassembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of double-strand break repair via homologous recombination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in replication fork processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in telomere maintenance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in telomere maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in telomere maintenance in response to DNA damage ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in telomeric loop disassembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in telomeric loop disassembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in telomeric loop disassembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in chromosome, telomeric region ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    regulator of telomere elongation helicase 1
    Names
    regulator of telomere length
    NP_001269938.1
    NP_001269939.1
    NP_057518.1
    NP_116575.3

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_033901.1 RefSeqGene

      Range
      5503..43436
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1149

    mRNA and Protein(s)

    1. NM_001283009.2NP_001269938.1  regulator of telomere elongation helicase 1 isoform 3

      See identical proteins and their annotated locations for NP_001269938.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest protein (isoform 3).
      Source sequence(s)
      AF217795, AW005229, JX119186
      Consensus CDS
      CCDS63331.1
      UniProtKB/TrEMBL
      R4IXY3
      Related
      ENSP00000353332.5, ENST00000360203.11
      Conserved Domains (3) summary
      PRK07764
      Location:9891240
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      cd13932
      Location:877976
      HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)
      TIGR00604
      Location:10743
      rad3; DNA repair helicase (rad3)
    2. NM_001283010.1NP_001269939.1  regulator of telomere elongation helicase 1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and has multiple coding region differences, compared to variant 3. These differences include translation initiation at a downstream AUG and a translational frameshift. The resulting protein (isoform 4) has a shorter N-terminus and distinct C-terminus, compared to isoform 3.
      Source sequence(s)
      AF217795, AK304798, AW005229
      Consensus CDS
      CCDS74751.1
      UniProtKB/Swiss-Prot
      Q9NZ71
      Related
      ENSP00000322287.5, ENST00000318100.9
      Conserved Domains (4) summary
      cd13932
      Location:654753
      HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)
      TIGR00604
      Location:2520
      rad3; DNA repair helicase (rad3)
      pfam13307
      Location:322508
      Helicase_C_2; Helicase C-terminal domain
      cl21455
      Location:149
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    3. NM_016434.4NP_057518.1  regulator of telomere elongation helicase 1 isoform 1

      See identical proteins and their annotated locations for NP_057518.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate splice site in the 3' coding region that results in a translational frameshift, compared to variant 3. The resulting protein (isoform 1) has a distinct C-terminus and is shorter than isoform 3.
      Source sequence(s)
      AF217795, AL353715
      Consensus CDS
      CCDS13531.1
      UniProtKB/Swiss-Prot
      A2A397, A2A398, B4DRM5, B4DYM3, B4E3N6, E1P5J4, E1P5J5, Q5JTV3, Q5JTV4, Q9BW37, Q9H402, Q9H4X6, Q9NX25, Q9NZ71, Q9NZ73, Q9UPR4, Q9Y4R6
      UniProtKB/TrEMBL
      R4IXY3
      Related
      ENSP00000359035.3, ENST00000370018.7
      Conserved Domains (5) summary
      cd13932
      Location:877976
      HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)
      TIGR00604
      Location:10743
      rad3; DNA repair helicase (rad3)
      pfam06733
      Location:111272
      DEAD_2; DEAD_2
      pfam13307
      Location:545731
      Helicase_C_2; Helicase C-terminal domain
      cl21455
      Location:1560
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    4. NM_032957.5NP_116575.3  regulator of telomere elongation helicase 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 3, one of which results in a translational frameshift. The encoded protein (isoform 2) has a distinct C-terminus and is shorter than isoform 3.
      Source sequence(s)
      AF217795, AK302508, AL353715
      Consensus CDS
      CCDS13530.3
      UniProtKB/TrEMBL
      R4IXY3
      Related
      ENSP00000424307.2, ENST00000508582.7
      Conserved Domains (5) summary
      cd13932
      Location:9011000
      HN_RTEL1; harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL)
      TIGR00604
      Location:10767
      rad3; DNA repair helicase (rad3)
      pfam06733
      Location:111296
      DEAD_2; DEAD_2
      pfam13307
      Location:569755
      Helicase_C_2; Helicase C-terminal domain
      cl21455
      Location:1560
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      63657810..63696253
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      65471931..65516559
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015647.2: Suppressed sequence

      Description
      NM_015647.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.