Human Gene RTEL1 (uc011abd.2) Description and Page Index
  Description: Homo sapiens regulator of telomere elongation helicase 1 (RTEL1), transcript variant 2, mRNA.
RefSeq Summary (NM_032957): 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].
Transcript (Including UTRs)
   Position: hg19 chr20:62,289,163-62,328,544 Size: 39,382 Total Exon Count: 35 Strand: +
Coding Region
   Position: hg19 chr20:62,290,756-62,327,138 Size: 36,383 Coding Exon Count: 34 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:62,289,163-62,328,544)mRNA (may differ from genome)Protein (1243 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIOMIM
PubMedReactomeStanford SOURCETreefamUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RTEL1
CDC HuGE Published Literature: RTEL1
Positive Disease Associations: Colitis, Ulcerative , Glioma
Related Studies:
  1. Colitis, Ulcerative
    Carl A Anderson et al. Nature genetics 2011, Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47., Nature genetics. [PubMed 21297633]
  2. Glioma
    Margaret Wrensch et al. Nature genetics 2009, Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility., Nature genetics. [PubMed 19578366]
  3. Glioma
    Margaret Wrensch et al. Nature genetics 2009, Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility., Nature genetics. [PubMed 19578366]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RTEL1
Diseases sorted by gene-association score: pulmonary fibrosis and/or bone marrow failure, telomere-related, 3* (1331), dyskeratosis congenita, autosomal recessive 5* (1231), dyskeratosis congenita* (572), rtel1-related dyskeratosis congenita* (500), pulmonary fibrosis, idiopathic* (175), dyskeratosis congenita autosomal recessive (30), pulmonary fibrosis (20), vestibulocochlear nerve disease (16), vestibular neuronitis (16), dyskeratosis congenita autosomal dominant (15), cerebellopontine angle tumor (9), vestibular disease (7), warsaw breakage syndrome (6), peripheral vertigo (6), middle ear disease (5), inner ear disease (4), aplastic anemia (2), auditory system disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.30 RPKM in Brain - Cerebellum
Total median expression: 19.22 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -365.40827-0.442 Picture PostScript Text
3' UTR -716.001406-0.509 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF06733 - DEAD_2
PF13307 - Helicase C-terminal domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9NZ71-7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AF217795 - Homo sapiens helicase-like protein NHL mRNA, complete cds.
JD339833 - Sequence 320857 from Patent EP1572962.
JD486643 - Sequence 467667 from Patent EP1572962.
JD462219 - Sequence 443243 from Patent EP1572962.
AK302508 - Homo sapiens cDNA FLJ61475 complete cds, highly similar to Regulator of telomere elongation helicase 1 (EC 3.6.1.-).
JD347207 - Sequence 328231 from Patent EP1572962.
AK304798 - Homo sapiens cDNA FLJ60225 complete cds, highly similar to Regulator of telomere elongation helicase 1(EC 3.6.1.-).
AK299332 - Homo sapiens cDNA FLJ57336 complete cds, highly similar to Regulator of telomere elongation helicase 1 (EC 3.6.1.-).
BC000673 - Homo sapiens mRNA similar to helicase-like protein NHL (cDNA clone IMAGE:3347926).
JD532733 - Sequence 513757 from Patent EP1572962.
BC131572 - Homo sapiens cDNA clone IMAGE:40108609, with apparent retained intron.
JX119186 - Homo sapiens regulator of telomere elongation helicase 1 isoform 3 (RTEL1) mRNA, complete cds.
AB384107 - Synthetic construct DNA, clone: pF1KSDA1088, Homo sapiens RTEL1 gene for tumor necrosis factor receptor superfamily member 6B precursor, complete cds, without stop codon, in Flexi system.
AB029011 - Homo sapiens KIAA1088 mRNA for KIAA1088 protein, partial cds.
AL157435 - Homo sapiens mRNA; cDNA DKFZp434O0510 (from clone DKFZp434O0510).
AK131105 - Homo sapiens mRNA for FLJ00362 protein.
AL080127 - Homo sapiens mRNA; cDNA DKFZp434C013 (from clone DKFZp434C013).
AK000485 - Homo sapiens cDNA FLJ20478 fis, clone KAT07359.
BC131817 - Homo sapiens potassium channel, subfamily K, member 4, mRNA (cDNA clone IMAGE:40122920).
AF217793 - Homo sapiens M68C mRNA, alternatively spliced, complete cds.
JD178003 - Sequence 159027 from Patent EP1572962.
JD068418 - Sequence 49442 from Patent EP1572962.
JD483563 - Sequence 464587 from Patent EP1572962.
JD334420 - Sequence 315444 from Patent EP1572962.
JD470509 - Sequence 451533 from Patent EP1572962.
JD143290 - Sequence 124314 from Patent EP1572962.
JD402530 - Sequence 383554 from Patent EP1572962.
JD193772 - Sequence 174796 from Patent EP1572962.
JD270443 - Sequence 251467 from Patent EP1572962.
JD456977 - Sequence 438001 from Patent EP1572962.
JD266853 - Sequence 247877 from Patent EP1572962.
JD386494 - Sequence 367518 from Patent EP1572962.
JD432315 - Sequence 413339 from Patent EP1572962.
JD515080 - Sequence 496104 from Patent EP1572962.
JD260253 - Sequence 241277 from Patent EP1572962.
JD310242 - Sequence 291266 from Patent EP1572962.
JD273462 - Sequence 254486 from Patent EP1572962.
JD401308 - Sequence 382332 from Patent EP1572962.
JD136689 - Sequence 117713 from Patent EP1572962.
JD441538 - Sequence 422562 from Patent EP1572962.
AF104419 - Homo sapiens decoy receptor 3 (DcR3) mRNA, complete cds.
AY358279 - Homo sapiens clone DNA30942 DcR3-TNFR (UNQ186) mRNA, complete cds.
BC017065 - Homo sapiens tumor necrosis factor receptor superfamily, member 6b, decoy, mRNA (cDNA clone MGC:9587 IMAGE:3886635), complete cds.
JD172760 - Sequence 153784 from Patent EP1572962.
JD056418 - Sequence 37442 from Patent EP1572962.
JD222755 - Sequence 203779 from Patent EP1572962.
BC034349 - Homo sapiens tumor necrosis factor receptor superfamily, member 6b, decoy, mRNA (cDNA clone MGC:21079 IMAGE:4752507), complete cds.
AF217794 - Homo sapiens M68E mRNA, alternatively spliced, complete cds.
AY124379 - Homo sapiens decoy receptor 3 variant 2 (TNFRSF6B) mRNA, partial cds; alternatively spliced.
AY124378 - Homo sapiens decoy receptor 3 variant 1 (TNFRSF6B) mRNA, complete cds; alternatively spliced.
JD470428 - Sequence 451452 from Patent EP1572962.
AB590899 - Synthetic construct DNA, clone: pFN21AE2246, Homo sapiens TNFRSF6B gene for tumor necrosis factor receptor superfamily, member 6b, decoy, without stop codon, in Flexi system.
KJ892617 - Synthetic construct Homo sapiens clone ccsbBroadEn_02011 TNFRSF6B gene, encodes complete protein.
AF134240 - Homo sapiens tumor necrosis factor receptor homolog (TR6) mRNA, complete cds.
JD533917 - Sequence 514941 from Patent EP1572962.
JD196537 - Sequence 177561 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NZ71 (Reactome details) participates in the following event(s):

R-HSA-5693589 D-loop dissociation and strand annealing
R-HSA-2564830 Cytosolic iron-sulfur cluster assembly
R-HSA-5693554 Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)
R-HSA-1430728 Metabolism
R-HSA-5693537 Resolution of D-Loop Structures
R-HSA-5685942 HDR through Homologous Recombination (HRR)
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693538 Homology Directed Repair
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: C20orf41, KIAA1088, NHL, NM_032957, NP_116575, Q9NZ71-7, uc021wge.1
UCSC ID: uc011abd.2
RefSeq Accession: NM_032957
Protein: Q9NZ71-7, splice isoform of Q9NZ71 CCDS: CCDS13530.3, CCDS13531.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RTEL1:
dkc (Dyskeratosis Congenita)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032957.4
exon count: 35CDS single in 3' UTR: no RNA size: 5042
ORF size: 3732CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6065.50frame shift in genome: no % Coverage: 99.70
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.