Human Gene HELLS (uc001kjt.3) Description and Page Index
  Description: Homo sapiens helicase, lymphoid-specific (HELLS), mRNA.
RefSeq Summary (NM_018063): This gene encodes a lymphoid-specific helicase. Other helicases function in processes involving DNA strand separation, including replication, repair, recombination, and transcription. This protein is thought to be involved with cellular proliferation and may play a role in leukemogenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2014].
Transcript (Including UTRs)
   Position: hg19 chr10:96,305,574-96,361,856 Size: 56,283 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr10:96,305,679-96,361,379 Size: 55,701 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:96,305,574-96,361,856)mRNA (may differ from genome)Protein (838 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Lymphoid-specific helicase; EC=3.6.4.-; AltName: Full=Proliferation-associated SNF2-like protein; AltName: Full=SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin subfamily A member 6;
FUNCTION: Plays an essential role in normal development and survival. Involved in regulation of the expansion or survival of lymphoid cells. Required for de novo or maintenance DNA methylation. May control silencing of the imprinted CDKN1C gene through DNA methylation. May play a role in formation and organization of heterochromatin, implying a functional role in the regulation of transcription and mitosis (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Closely associated with pericentric heterochromatin (By similarity).
TISSUE SPECIFICITY: Highly expressed in proliferative tissues such as adult thymus and testis, and expressed at lower levels in uterus, small intestine, colon, and peripheral blood mononuclear cells. Also expressed in neoplastic cell lines including those derived from myeloid and lymphoid leukemias.
INDUCTION: By concanavalin-A in peripheral blood leukocytes.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=AAG01987.1; Type=Erroneous initiation; Sequence=AAH29381.1; Type=Erroneous initiation; Sequence=AAH30963.1; Type=Erroneous initiation; Sequence=AAH31004.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HELLS
CDC HuGE Published Literature: HELLS
Positive Disease Associations: Acenocoumarol , Ticlopidine
Related Studies:
  1. Acenocoumarol
    Martina Teichert et al. Human molecular genetics 2009, A genome-wide association study of acenocoumarol maintenance dosage., Human molecular genetics. [PubMed 19578179]
  2. Ticlopidine
    Alan R Shuldiner et al. JAMA : the journal of the American Medical Association 2009, Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy., JAMA : the journal of the American Medical Association. [PubMed 19706858]
    CYP2C19*2 genotype was associated with diminished platelet response to clopidogrel treatment and poorer cardiovascular outcomes.

-  MalaCards Disease Associations
  MalaCards Gene Search: HELLS
Diseases sorted by gene-association score: immunodeficiency-centromeric instability-facial anomalies syndrome 4* (930), immunodeficiency-centromeric instability-facial anomalies syndrome* (199), alpha-thalassemia/mental retardation syndrome (20), rothmund-thomson syndrome (11), japanese encephalitis (11), werner syndrome (10), rapadilino syndrome (10), bloom syndrome (10), cockayne syndrome (8), thalassemias, alpha- (8), xeroderma pigmentosum, group b (8), trichothiodystrophy 1, photosensitive (7), spondylosis (6), compartment syndrome (5), fanconi anemia, complementation group a (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • C006253 pirinixic acid
  • C025223 1,4-dioxane
  • D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine
  • C495626 14-deoxy-11,12-didehydroandrographolide
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C027576 4-hydroxy-2-nonenal
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
          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: 12.16 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 49.45 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.90105-0.399 Picture PostScript Text
3' UTR -102.00477-0.214 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
  InterPro Domains: Graphical view of domain structure
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N

Pfam Domains:
PF00176 - SNF2 family N-terminal domain
PF00271 - Helicase conserved C-terminal domain
PF04851 - Type III restriction enzyme, res subunit

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

ModBase Predicted Comparative 3D Structure on Q9NRZ9
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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0006346 methylation-dependent chromatin silencing
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007049 cell cycle
GO:0007275 multicellular organism development
GO:0010216 maintenance of DNA methylation
GO:0031508 pericentric heterochromatin assembly
GO:0046651 lymphocyte proliferation
GO:0051301 cell division

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0005634 nucleus
GO:0005721 pericentric heterochromatin

-  Descriptions from all associated GenBank mRNAs
  AK314485 - Homo sapiens cDNA, FLJ95293, Homo sapiens helicase, lymphoid-specific (HELLS), mRNA.
BX538033 - Homo sapiens mRNA; cDNA DKFZp686J0676 (from clone DKFZp686J0676); complete cds.
BC068440 - Homo sapiens cDNA clone IMAGE:4824050, containing frame-shift errors.
AF155827 - Homo sapiens proliferation-associated SNF2-like protein (SMARCA6) mRNA, complete cds.
BC111789 - Homo sapiens cDNA clone IMAGE:40019490, containing frame-shift errors.
AB527159 - Synthetic construct DNA, clone: pF1KB7327, Homo sapiens HELLS gene for helicase, lymphoid-specific, without stop codon, in Flexi system.
BC146308 - Synthetic construct Homo sapiens clone IMAGE:100015232, MGC:180256 helicase, lymphoid-specific (HELLS) mRNA, encodes complete protein.
AB102716 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant1, complete cds.
AB102717 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant2, complete cds.
AB102718 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant3, complete cds.
AB102719 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant4, complete cds.
AB102720 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant5, complete cds.
AB102721 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant6, complete cds.
AB102722 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant7, complete cds.
AB102723 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant8, complete cds.
AB113248 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant9, complete cds.
AB113249 - Homo sapiens HELLS mRNA for lymphoid specific helicase variant10, complete cds.
EU831945 - Synthetic construct Homo sapiens clone HAIB:100066974; DKFZo008D1023 helicase, lymphoid-specific protein (HELLS) gene, encodes complete protein.
EU832040 - Synthetic construct Homo sapiens clone HAIB:100067069; DKFZo004D1024 helicase, lymphoid-specific protein (HELLS) gene, encodes complete protein.
AK308331 - Homo sapiens cDNA, FLJ98279.
BC105606 - Homo sapiens helicase, lymphoid-specific, mRNA (cDNA clone IMAGE:6725530), partial cds.
JD184473 - Sequence 165497 from Patent EP1572962.
JD519101 - Sequence 500125 from Patent EP1572962.
JD125979 - Sequence 107003 from Patent EP1572962.
AK022928 - Homo sapiens cDNA FLJ12866 fis, clone NT2RP2003691.
BC030963 - Homo sapiens helicase, lymphoid-specific, mRNA (cDNA clone IMAGE:4109340), complete cds.
BC031004 - Homo sapiens helicase, lymphoid-specific, mRNA (cDNA clone IMAGE:4108169), complete cds.
AY007108 - Homo sapiens clone TCCCTA00017 mRNA sequence.
AB074174 - Homo sapiens primary neuroblastoma cDNA, clone:Nbla10143, full insert sequence.
JD553922 - Sequence 534946 from Patent EP1572962.
BC029381 - Homo sapiens helicase, lymphoid-specific, mRNA (cDNA clone IMAGE:4738004), complete cds.
CU689054 - Synthetic construct Homo sapiens gateway clone IMAGE:100022219 5' read HELLS mRNA.
KJ901477 - Synthetic construct Homo sapiens clone ccsbBroadEn_10871 HELLS gene, encodes complete protein.
BC015477 - Homo sapiens helicase, lymphoid-specific, mRNA (cDNA clone IMAGE:3913594), partial cds.
AK001201 - Homo sapiens cDNA FLJ10339 fis, clone NT2RM2000740, weakly similar to POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L.
JD524022 - Sequence 505046 from Patent EP1572962.
JD504202 - Sequence 485226 from Patent EP1572962.
JD326497 - Sequence 307521 from Patent EP1572962.
JD553085 - Sequence 534109 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RB41, HELLS_HUMAN, Nbla10143, NM_018063, NP_060533, PASG, Q3LID1, Q6I7N7, Q76H76, Q76H77, Q76H78, Q76H79, Q76H80, Q76H81, Q7Z397, Q7Z5X2, Q8N6P4, Q9H4P5, Q9NRZ9, SMARCA6
UCSC ID: uc001kjt.3
RefSeq Accession: NM_018063
Protein: Q9NRZ9 (aka HELLS_HUMAN)
CCDS: CCDS7434.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_018063.3
exon count: 22CDS single in 3' UTR: no RNA size: 3165
ORF size: 2517CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5231.00frame shift in genome: no % Coverage: 97.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.