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

Gene ID: 51750, updated on 19-Feb-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
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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.