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Hltf helicase-like transcription factor [ Mus musculus (house mouse) ]

Gene ID: 20585, updated on 9-Dec-2024

Summary

Official Symbol
Hltfprovided by MGI
Official Full Name
helicase-like transcription factorprovided by MGI
Primary source
MGI:MGI:1196437
See related
Ensembl:ENSMUSG00000002428 AllianceGenome:MGI:1196437
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
P113; Snf2l3; Smarca3
Summary
Enables ATP-dependent activity, acting on DNA. Involved in mRNA transcription by RNA polymerase II; positive regulation of transcription by RNA polymerase II; and regulation of neurogenesis. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including central nervous system; early conceptus; genitourinary system; intestine; and sensory organ. Orthologous to human HLTF (helicase like transcription factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in bladder adult (RPKM 4.7), placenta adult (RPKM 4.5) and 28 other tissues See more
Orthologs
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Genomic context

See Hltf in Genome Data Viewer
Location:
3 A2; 3 6.15 cM
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (20111959..20172655)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (20057808..20118491)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 42190 Neighboring gene ceruloplasmin Neighboring gene STARR-seq mESC enhancer starr_07104 Neighboring gene STARR-seq mESC enhancer starr_07105 Neighboring gene STARR-positive B cell enhancer ABC_E3428 Neighboring gene HPS3, biogenesis of lysosomal organelles complex 2 subunit 1 Neighboring gene STARR-seq mESC enhancer starr_07106 Neighboring gene STARR-seq mESC enhancer starr_07107 Neighboring gene STARR-positive B cell enhancer ABC_E1018 Neighboring gene STARR-seq mESC enhancer starr_07108 Neighboring gene VISTA enhancer mm86 Neighboring gene glycogenin 1 Neighboring gene STARR-seq mESC enhancer starr_07112 Neighboring gene STARR-seq mESC enhancer starr_07113 Neighboring gene predicted gene, 31320 Neighboring gene microRNA 7007 Neighboring gene carboxypeptidase A3, mast cell

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding  
enables ATP-dependent activity, acting on DNA  
enables ATP-dependent activity, acting on DNA PubMed 
enables DNA binding  
enables helicase activity  
enables hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides  
enables transferase activity  
enables ubiquitin protein ligase activity  
enables ubiquitin protein ligase binding PubMed 
enables zinc ion binding  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex PubMed 
part_of RNA polymerase II transcription regulator complex  
located_in cytoplasm  
located_in nuclear matrix PubMed 
located_in nucleolus  
located_in nucleoplasm  
located_in nucleoplasm  
is_active_in nucleus  

General protein information

Preferred Names
helicase-like transcription factor
Names
RING-type E3 ubiquitin transferase HLTF
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3
TNF-response element-binding protein
sucrose nonfermenting protein 2-like 3
NP_001342026.1
NP_033236.2
XP_006535492.1
XP_036018883.1

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.

mRNA and Protein(s)

  1. NM_001355097.1NP_001342026.1  helicase-like transcription factor

    Status: VALIDATED

    Source sequence(s)
    AC073883, AC079442, AC158937
    Consensus CDS
    CCDS17261.1
    UniProtKB/Swiss-Prot
    O35596, O35597, Q6PCN7, Q80VT6
    Conserved Domains (3) summary
    COG0553
    Location:4721003
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    pfam08797
    Location:60153
    HIRAN; HIRAN domain
    cd16509
    Location:752795
    RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins
  2. NM_009210.3NP_033236.2  helicase-like transcription factor

    See identical proteins and their annotated locations for NP_033236.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the functional protein.
    Source sequence(s)
    BB007413, BC059240, BY007037
    Consensus CDS
    CCDS17261.1
    UniProtKB/Swiss-Prot
    O35596, O35597, Q6PCN7, Q80VT6
    Related
    ENSMUSP00000002502.6, ENSMUST00000002502.12
    Conserved Domains (3) summary
    COG0553
    Location:4721003
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    pfam08797
    Location:60153
    HIRAN; HIRAN domain
    cd16509
    Location:752795
    RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins

RNA

  1. NR_105046.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC079442, AK166911, BB007413, BC059240, BY007037
  2. NR_105047.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has different structures at the 5' and 3' ends and lacks two alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK149897, BB007413
    Related
    ENSMUST00000145853.8

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    20111959..20172655
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006535429.4XP_006535492.1  helicase-like transcription factor isoform X1

    Conserved Domains (3) summary
    COG0553
    Location:329860
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd16509
    Location:609652
    RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins
    cd18071
    Location:97495
    DEXHc_HLTF1_SMARC3; DEXH-box helicase domain of HLTF1
  2. XM_036162990.1XP_036018883.1  helicase-like transcription factor isoform X2

    Conserved Domains (3) summary
    COG0553
    Location:129660
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd16509
    Location:409452
    RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins
    cl28899
    Location:129295
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

RNA

  1. XR_001783674.3 RNA Sequence

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