Format

Send to:

Choose Destination

HLTF helicase like transcription factor [ Homo sapiens (human) ]

Gene ID: 6596, updated on 18-Nov-2019

Summary

Official Symbol
HLTFprovided by HGNC
Official Full Name
helicase like transcription factorprovided by HGNC
Primary source
HGNC:HGNC:11099
See related
Ensembl:ENSG00000071794 MIM:603257
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
ZBU1; HLTF1; RNF80; HIP116; SNF2L3; HIP116A; SMARCA3
Summary
This gene encodes a member of the SWI/SNF family. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein contains a RING finger DNA binding motif. Two transcript variants encoding the same protein have been found for this gene. However, use of an alternative translation start site produces an isoform that is truncated at the N-terminus compared to the full-length protein. [provided by RefSeq, Jul 2008]
Expression
Broad expression in testis (RPKM 29.4), adrenal (RPKM 14.1) and 25 other tissues See more
Orthologs

Genomic context

See HLTF in Genome Data Viewer
Location:
3q24
Exon count:
25
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (149030063..149086554, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (148747904..148804341, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ubiquilin 4 pseudogene 1 Neighboring gene glycogenin 1 Neighboring gene HLTF antisense RNA 1 Neighboring gene mediator complex subunit 28 pseudogene 2 Neighboring gene HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 Neighboring gene ceruloplasmin

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef upregulates the expression of helicase-like transcription factor (HLTF-1) in HeLa cells PubMed
Vpr vpr HIV-1 Vpr downregulates HLTF in a DCAF1-dependent manner in HeLa, Jurkat T and primary T cells and primary macrophages as shown through DCAF1 siRNA knockdown PubMed
vpr HIV-1 Vpr specifically binds HLTF and recruits it to the DCAF1-DDB1 module of the CRL4-DCAF1 E3 complex, thereby directing HLTF for degradation by proteasome PubMed
vpr HIV-1 Vpr recruits HLTF for proteasome-dependent degradation via CRL4-DCAF1 E3 PubMed
vpr HIV-1 Vpr downregulates HLTF (CEM.SS-iH1.Vpr and U2OS-iH1.Vpr cells), a post-replication DNA helicase, independently of cell cycle position and of MUS81 depletion and independent of UNG2, yet all three require DCAF1 PubMed
vpr HIV-1 Vpr downregulates HLTF in infected HeLa, T cells and primary macrophages in a proteasome-dependent manner (in HeLa cells) and independent of Vpr-mediated G2 arrest in HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
DNA-dependent ATPase activity IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
RNA polymerase II proximal promoter sequence-specific DNA 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 
ubiquitin protein ligase activity EXP
Inferred from Experiment
more info
PubMed 
ubiquitin protein ligase binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
protein ubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein ubiquitination TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
helicase-like transcription factor
Names
DNA-binding protein/plasminogen activator inhibitor-1 regulator
RING finger protein 80
RING-type E3 ubiquitin transferase HLTF
SNF2-like 3
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3
sucrose nonfermenting protein 2-like 3
sucrose nonfermenting-like 3
NP_001305863.1
NP_001305864.1
NP_003062.2
NP_620636.1
XP_011511393.1
XP_011511394.1
XP_011511395.1
XP_016862567.1
XP_016862568.1

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.

mRNA and Protein(s)

  1. NM_001318934.1NP_001305863.1  helicase-like transcription factor isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC021059, BC044659
    Consensus CDS
    CCDS82856.1
    UniProtKB/Swiss-Prot
    Q14527
    UniProtKB/TrEMBL
    A0A0C4DGA6
    Related
    ENSP00000420745.1, ENST00000465259.5
    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:477587
    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.
    cd00162
    Location:758803
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:471721
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:831949
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  2. NM_001318935.2NP_001305864.1  helicase-like transcription factor isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AC021059, AK291231
    Consensus CDS
    CCDS33875.1
    UniProtKB/Swiss-Prot
    Q14527
    UniProtKB/TrEMBL
    A8K5B6
    Related
    ENSP00000420429.1, ENST00000494055.5
    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:478588
    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.
    cd00162
    Location:759804
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:472722
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:832950
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  3. NM_003071.4NP_003062.2  helicase-like transcription factor isoform 1

    See identical proteins and their annotated locations for NP_003062.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AC021059, AI971472, BC030976, BC044659, L34673
    Consensus CDS
    CCDS33875.1
    UniProtKB/Swiss-Prot
    Q14527
    UniProtKB/TrEMBL
    Q05BZ6
    Related
    ENSP00000308944.5, ENST00000310053.10
    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:478588
    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.
    cd00162
    Location:759804
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:472722
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:832950
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  4. NM_139048.3NP_620636.1  helicase-like transcription factor isoform 1

    See identical proteins and their annotated locations for NP_620636.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AC021059, AI971472, BC030976, L34673
    Consensus CDS
    CCDS33875.1
    UniProtKB/Swiss-Prot
    Q14527
    UniProtKB/TrEMBL
    Q05BZ6
    Related
    ENSP00000376644.2, ENST00000392912.6
    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:478588
    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.
    cd00162
    Location:759804
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:472722
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:832950
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    149030063..149086554 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513091.2XP_011511393.1  helicase-like transcription factor isoform X1

    See identical proteins and their annotated locations for XP_011511393.1

    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:478588
    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.
    cd00162
    Location:763808
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:472722
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:836954
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  2. XM_017007079.2XP_016862568.1  helicase-like transcription factor isoform X3

    UniProtKB/Swiss-Prot
    Q14527
    UniProtKB/TrEMBL
    A0A0C4DGA6
    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:477587
    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.
    cd00162
    Location:758803
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:471721
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:831949
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  3. XM_017007078.1XP_016862567.1  helicase-like transcription factor isoform X2

    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:477587
    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.
    cd00162
    Location:762807
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:471721
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:835953
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  4. XM_011513093.2XP_011511395.1  helicase-like transcription factor isoform X2

    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:477587
    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.
    cd00162
    Location:762807
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:471721
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:835953
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
  5. XM_011513092.2XP_011511394.1  helicase-like transcription factor isoform X1

    See identical proteins and their annotated locations for XP_011511394.1

    Conserved Domains (6) summary
    smart00487
    Location:238320
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:478588
    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.
    cd00162
    Location:763808
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam00176
    Location:472722
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:836954
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60155
    HIRAN; HIRAN domain
Support Center