HELLS helicase, lymphoid specific [Homo sapiens (human)] - Gene

Summary

Official Symbol: HELLSprovided by HGNC
Official Full Name: helicase, lymphoid specificprovided by HGNC
Primary source: HGNC:HGNC:4861
See related: Ensembl:ENSG00000119969 MIM:603946; AllianceGenome:HGNC:4861
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: LSH; ICF4; PASG; SALNR; SMARCA6; Nbla10143
Summary: 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]
Annotation information: Note: The sequence defining GeneID 220513, which was based on XM_017508.4 and annotated on 12q13.12, currently corresponds to this locus. [08 Feb 2009]
Expression: Broad expression in testis (RPKM 2.1), bone marrow (RPKM 1.7) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q23.33

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (94545788..94613905)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (95424900..95493015)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (96305545..96361856)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models.
Title: Lost in HELLS: Disentangling the mystery of SALNR existence in senescence cellular models.
The Chromatin Remodeler HELLS: A New Regulator in DNA Repair, Genome Maintenance, and Cancer.
Title: The Chromatin Remodeler HELLS: A New Regulator in DNA Repair, Genome Maintenance, and Cancer.
Diagnostic, Prognostic, and Immunological Roles of HELLS in Pan-Cancer: A Bioinformatics Analysis.
Title: Diagnostic, Prognostic, and Immunological Roles of HELLS in Pan-Cancer: A Bioinformatics Analysis.
Hsa_circ_0072008 regulates cell proliferation, migration, and invasion in cervical squamous cell carcinoma via miR-1305/helicase, lymphoid specific (HELLS) axis.
Title: Hsa_circ_0072008 regulates cell proliferation, migration, and invasion in cervical squamous cell carcinoma via miR-1305/helicase, lymphoid specific (HELLS) axis.
Lymphoid-specific helicase in epigenetics, DNA repair and cancer.
Title: Lymphoid-specific helicase in epigenetics, DNA repair and cancer.
Suppression of HELLS by miR-451a represses mTOR pathway to hinder aggressiveness of SCLC.
Title: Suppression of HELLS by miR-451a represses mTOR pathway to hinder aggressiveness of SCLC.
The cross-talk between methylation and phosphorylation in lymphoid-specific helicase drives cancer stem-like properties.
Title: The cross-talk between methylation and phosphorylation in lymphoid-specific helicase drives cancer stem-like properties.
The DNA-helicase HELLS drives ALK(-) ALCL proliferation by the transcriptional control of a cytokinesis-related program.
Title: The DNA-helicase HELLS drives ALK(-) ALCL proliferation by the transcriptional control of a cytokinesis-related program.
CDCA7 and HELLS suppress DNA:RNA hybrid-associated DNA damage at pericentromeric repeats.
Title: CDCA7 and HELLS suppress DNA:RNA hybrid-associated DNA damage at pericentromeric repeats.
A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1 chromatin association.
Title: A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1 chromatin association.

Submit: New GeneRIF Correction See all GeneRIFs (35)

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

Associated conditions

Description	Tests
Immunodeficiency-centromeric instability-facial anomalies syndrome 4 MedGen: C4310798 OMIM: 616911 GeneReviews: Not available	Compare labs

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

RH93667 (e-PCR)
- UniSTS:89876

STS-N95450 (e-PCR)
- UniSTS:69683

GDB:631813 (e-PCR)
- UniSTS:158430

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	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 methylation-dependent heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA methylation-dependent heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in kidney development	ISS Inferred from Sequence or Structural Similarity more info
involved_in lymphocyte proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in lymphocyte proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of intrinsic apoptotic signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in pericentric heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in pericentric heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in urogenital system development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of pericentric heterochromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of pericentric heterochromatin	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: lymphoid-specific helicase

Names: SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6; Senescence Associated Long Non-coding RNA; proliferation-associated SNF2-like protein

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

NG_047057.2 RefSeqGene

Range

5002..61313

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001289067.2 → NP_001275996.1 lymphoid-specific helicase isoform 2

See identical proteins and their annotated locations for NP_001275996.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate in-frame exon, compared to variant 1. The encoded protein (isoform 2) is longer, compared to isoform 1.

Source sequence(s)

AB102723, BC015477, BC105606, BC111789, DC423372

Consensus CDS

CCDS73162.1

UniProtKB/TrEMBL

A0A0B4J1V9, Q6I7N8

Related

ENSP00000377601.2, ENST00000394036.6

Conserved Domains (3) summary

cd00046
Location:243 → 385

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:640 → 766

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:226 → 623

SNF2_N; SNF2 family N-terminal domain
NM_001289068.2 → NP_001275997.1 lymphoid-specific helicase isoform 3

See identical proteins and their annotated locations for NP_001275997.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 3) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

BC015477, BC068440, BC111789, BX538033

Consensus CDS

CCDS91308.1

UniProtKB/TrEMBL

Q6I7N8

Related

ENSP00000409945.2, ENST00000419900.6

Conserved Domains (3) summary

cd00046
Location:227 → 369

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:578 → 704

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:210 → 561

SNF2_N; SNF2 family N-terminal domain
NM_001289069.2 → NP_001275998.1 lymphoid-specific helicase isoform 4

See identical proteins and their annotated locations for NP_001275998.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate in-frame splice site compared to variant 1. The encoded protein (isoform 4) is shorter, compared to isoform 1.

Source sequence(s)

AB102718, BC015477, BC105606, BC111789, DC423372

Consensus CDS

CCDS91306.1

UniProtKB/TrEMBL

Q6I7N8

Related

ENSP00000513940.1, ENST00000698675.1

Conserved Domains (3) summary

cd00046
Location:243 → 353

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:562 → 688

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:226 → 545

SNF2_N; SNF2 family N-terminal domain
NM_001289070.2 → NP_001275999.1 lymphoid-specific helicase isoform 5

See identical proteins and their annotated locations for NP_001275999.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two alternate in-frame exons compared to variant 1. The encoded protein (isoform 5) is shorter, compared to isoform 1.

Source sequence(s)

AB102721, BC015477, BC105606, BC111789, DC423372

Consensus CDS

CCDS73163.1

UniProtKB/TrEMBL

Q6I7N8

Related

ENSP00000377609.1, ENST00000394045.6

Conserved Domains (3) summary

cd00046
Location:243 → 339

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:496 → 622

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:226 → 479

SNF2_N; SNF2 family N-terminal domain
NM_001289071.2 → NP_001276000.1 lymphoid-specific helicase isoform 6

See identical proteins and their annotated locations for NP_001276000.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) contains an alternate exon and differs in the 5' UTR, and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 6) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AB102716, AL138759, BC015477, BC105606

UniProtKB/TrEMBL

Q6I7N8

Conserved Domains (3) summary

cd00046
Location:119 → 261

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:470 → 596

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:102 → 453

SNF2_N; SNF2 family N-terminal domain
NM_001289072.2 → NP_001276001.1 lymphoid-specific helicase isoform 7

See identical proteins and their annotated locations for NP_001276001.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate in-frame splice site and lacks two alternate in-frame exons compared to variant 1. The encoded protein (isoform 7) is shorter compared to isoform 1.

Source sequence(s)

AB102719, BC015477, BC105606, BC111789, DC423372

Consensus CDS

CCDS91307.1

UniProtKB/TrEMBL

Q6I7N8

Related

ENSP00000513942.1, ENST00000698799.1

Conserved Domains (3) summary

cd00046
Location:243 → 325

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:464 → 590

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:226 → 447

SNF2_N; SNF2 family N-terminal domain
NM_001289073.2 → NP_001276002.1 lymphoid-specific helicase isoform 8

See identical proteins and their annotated locations for NP_001276002.1

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks an alternate exon in the 5' coding region and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 8) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AB102717, BC015477, BC105606, BC111789, DC423372

UniProtKB/TrEMBL

A0A087WSW7, Q6I7N8

Conserved Domains (3) summary

cd00046
Location:105 → 247

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:456 → 582

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:88 → 439

SNF2_N; SNF2 family N-terminal domain
NM_001289074.2 → NP_001276003.1 lymphoid-specific helicase isoform 9

Status: REVIEWED

Description

Transcript Variant: This variant (9) uses an alternate splice site and lacks an alternate exon in the 5' coding region, and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 9) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AB102722, BC015477, BC105606, BC111789, DC423372

UniProtKB/TrEMBL

F6RPV8

Conserved Domains (1) summary

cd00079
Location:233 → 359

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
NM_001289075.2 → NP_001276004.1 lymphoid-specific helicase isoform 10

See identical proteins and their annotated locations for NP_001276004.1

Status: REVIEWED

Description

Transcript Variant: This variant (10) lacks an exon in the 5' coding region and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 10) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AB102720, BC015477, BC105606, BC111789, DC423372

UniProtKB/TrEMBL

F6RPV8

Related

ENSP00000360378.2, ENST00000371327.3

Conserved Domains (1) summary

cd00079
Location:188 → 314

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
NM_018063.5 → NP_060533.2 lymphoid-specific helicase isoform 1

See identical proteins and their annotated locations for NP_060533.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AF155827, AK314485, BC015477, BC111789

Consensus CDS

CCDS7434.1

UniProtKB/Swiss-Prot

B2RB41, Q3LID1, Q6I7N7, Q76H76, Q76H77, Q76H78, Q76H79, Q76H80, Q76H81, Q7Z397, Q7Z5X2, Q8N6P4, Q9H4P5, Q9NRZ9

UniProtKB/TrEMBL

Q6I7N8

Related

ENSP00000239027.7, ENST00000348459.10

Conserved Domains (3) summary

cd00046
Location:243 → 385

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00079
Location:594 → 720

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

pfam00176
Location:226 → 577

SNF2_N; SNF2 family N-terminal domain