Format

Send to:

Choose Destination

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

Gene ID: 3070, updated on 12-Aug-2018

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; Vega:OTTHUMG00000018793
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; 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

Genomic context

See HELLS in Genome Data Viewer
Location:
10q23.33
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (94545767..94613905)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (96305535..96362628)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene phospholipase C epsilon 1 Neighboring gene NOC3 like DNA replication regulator Neighboring gene TBC1 domain family member 12 Neighboring gene C-terminal binding protein 2 pseudogene 2 Neighboring gene cytochrome P450 family 2 subfamily C member 18

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10339

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
helicase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
lymphocyte proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
maintenance of DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
methylation-dependent chromatin silencing ISS
Inferred from Sequence or Structural Similarity
more info
 
multicellular organism development ISS
Inferred from Sequence or Structural Similarity
more info
 
pericentric heterochromatin assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
lymphoid-specific helicase
Names
SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6
proliferation-associated SNF2-like protein

NCBI Reference Sequences (RefSeq)

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_047057.1 RefSeqGene

    Range
    5001..61333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001289067.1NP_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/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    A0A0B4J1V9, Q0VGL2
    Related
    ENSP00000377601.2, ENST00000394036.5
    Conserved Domains (3) summary
    cd00046
    Location:243385
    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:640766
    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:226623
    SNF2_N; SNF2 family N-terminal domain
  2. NM_001289068.1NP_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)
    AL138759, BC015477, BC068440, BC111789, BX538033
    UniProtKB/Swiss-Prot
    Q9NRZ9
    Conserved Domains (3) summary
    cd00046
    Location:227369
    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:578704
    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:210561
    SNF2_N; SNF2 family N-terminal domain
  3. NM_001289069.1NP_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
    UniProtKB/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    Q0VGL2
    Conserved Domains (3) summary
    cd00046
    Location:243353
    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:562688
    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:226545
    SNF2_N; SNF2 family N-terminal domain
  4. NM_001289070.1NP_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/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    Q0VGL2
    Related
    ENSP00000377609.1, ENST00000394045.5
    Conserved Domains (3) summary
    cd00046
    Location:243339
    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:496622
    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:226479
    SNF2_N; SNF2 family N-terminal domain
  5. NM_001289071.1NP_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
    Consensus CDS
    CCDS73165.1
    UniProtKB/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    F6XU50, Q0VGL2, Q76H82
    Related
    ENSP00000239026.7, ENST00000239026.10
    Conserved Domains (3) summary
    cd00046
    Location:119261
    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:470596
    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:102453
    SNF2_N; SNF2 family N-terminal domain
  6. NM_001289072.1NP_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
    UniProtKB/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    Q0VGL2
    Conserved Domains (3) summary
    cd00046
    Location:243325
    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:464590
    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:226447
    SNF2_N; SNF2 family N-terminal domain
  7. NM_001289073.1NP_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
    Consensus CDS
    CCDS73164.1
    UniProtKB/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    A0A087WSW7, Q0VGL2
    Related
    ENSP00000360383.5, ENST00000371332.8
    Conserved Domains (3) summary
    cd00046
    Location:105247
    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:456582
    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:88439
    SNF2_N; SNF2 family N-terminal domain
  8. NM_001289074.1NP_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/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    Q0VGL2
    Conserved Domains (1) summary
    cd00079
    Location:233359
    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 ...
  9. NM_001289075.1NP_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/Swiss-Prot
    Q9NRZ9
    UniProtKB/TrEMBL
    Q0VGL2
    Conserved Domains (1) summary
    cd00079
    Location:188314
    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 ...
  10. NM_018063.4NP_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, AL138759, BC015477, BC111789
    Consensus CDS
    CCDS7434.1
    UniProtKB/Swiss-Prot
    Q9NRZ9
    Related
    ENSP00000239027.7, OTTHUMP00000020127, ENST00000348459.9, OTTHUMT00000049475
    Conserved Domains (3) summary
    cd00046
    Location:243385
    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:594720
    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:226577
    SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    94545767..94613905
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447968.1XP_024303736.1  lymphoid-specific helicase isoform X2

  2. XM_024447967.1XP_024303735.1  lymphoid-specific helicase isoform X1

    Conserved Domains (1) summary
    cl26465
    Location:1601
    SNF2_N; SNF2 family N-terminal domain
Support Center