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

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, Jul 2025]
Expression: Ubiquitous expression in bladder adult (RPKM 4.7), placenta adult (RPKM 4.5) and 28 other tissues See more
Orthologs: all
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Genomic context

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_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic beta cells resulting in neonatal lethality.
Title: Helicase-like transcription factor (Hltf)-deletion activates Hmgb1-Rage axis and granzyme A-mediated killing of pancreatic β cells resulting in neonatal lethality.
Activation of the p11/SMARCA3/Neurensin-2 pathway in parvalbumin interneurons mediates the response to chronic antidepressants.
Title: Activation of the p11/SMARCA3/Neurensin-2 pathway in parvalbumin interneurons mediates the response to chronic antidepressants.
This is the first study to show Hltf-deletion in an inflammation-associated colorectal cancer model elevates mitochondrial bioenergetics.
Title: Helicase-like transcription factor (Hltf) gene-deletion promotes oxidative phosphorylation (OXPHOS) in colorectal tumors of AOM/DSS-treated mice.
Findings 1) prove the truncated Hltf protein isoform is a transcription factor, 2) establish a functional link between AS of Hltf and immunosuppression at the feto-maternal interface, 3) correlate intron retention with the absence of DNA methylation, and 4) underscore the importance of differential splicing analysis to identify Hltf's functional diversity.
Title: Alternative splicing of helicase-like transcription factor (Hltf): Intron retention-dependent activation of immune tolerance at the feto-maternal interface.
silencing Hltf during heart organogenesis compromised DNA double-strand break repair, and caused aberrant collagen biogenesis altering the structural network that transmits cardiomyocyte force into muscle contraction
Title: Helicase-like transcription factor (Hltf) regulates G2/M transition, Wt1/Gata4/Hif-1a cardiac transcription networks, and collagen biogenesis.
Data show a role of helicase-like transcription factor (hltf) in the G2/m transition and apoptosis in brain
Title: Role of helicase-like transcription factor (hltf) in the G2/m transition and apoptosis in brain.
p11 and AnxA2 cooperate to create a unique binding pocket, but the optimal binding condition is not achieved without conformational changes associated with target binding. Upon interaction with the SMARCA3 peptide, both Asp60 in p11 and Ser12 in AnxA2 flip inward toward the peptide-binding groove, forming additional intermolecular hydrogen bonds.
Title: SMARCA3, a chromatin-remodeling factor, is required for p11-dependent antidepressant action.
Results demonstrate that loss of HLTF function promotes the malignant transformation of intestinal or colonic adenomas to carcinomas by inducing genomic instability.
Title: Loss of HLTF function promotes intestinal carcinogenesis.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (3)
Spontaneous (1) 1 citation
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent activity, acting on DNA	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent activity, acting on DNA	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	ISO Inferred from Sequence Orthology more info
enables DNA translocase activity	IEA Inferred from Electronic Annotation more info
enables DNA translocase activity	ISO Inferred from Sequence Orthology more info
enables DNA translocase activity	ISS Inferred from Sequence or Structural Similarity more info
enables G-quadruplex unwinding activity	IEA Inferred from Electronic Annotation more info
enables G-quadruplex unwinding activity	ISO Inferred from Sequence Orthology more info
enables histone H3K23 ubiquitin ligase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K23 ubiquitin ligase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K23 ubiquitin ligase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K9me2/3 reader activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9me2/3 reader activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9me2/3 reader activity	ISS Inferred from Sequence or Structural Similarity more info
enables hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromosomal DNA methylation maintenance following DNA replication	IEA Inferred from Electronic Annotation more info
involved_in chromosomal DNA methylation maintenance following DNA replication	ISO Inferred from Sequence Orthology more info
involved_in chromosomal DNA methylation maintenance following DNA replication	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K63-linked ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K63-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein K63-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to chromatin	IEA Inferred from Electronic Annotation more info
involved_in protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in protein localization to chromatin	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein polyubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein polyubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of neurogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in replication fork reversal	IEA Inferred from Electronic Annotation more info
involved_in replication fork reversal	ISO Inferred from Sequence Orthology more info
involved_in replication fork reversal	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
is_active_in chromatin	IEA Inferred from Electronic Annotation more info
is_active_in chromatin	ISO Inferred from Sequence Orthology more info
is_active_in chromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome	ISO Inferred from Sequence Orthology more info
located_in chromosome	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nuclear replication fork	IEA Inferred from Electronic Annotation more info
located_in nuclear replication fork	ISO Inferred from Sequence Orthology more info
located_in nuclear replication fork	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	EXP Inferred from Experiment more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA-dependent ATPase/E3 ubiquitin-protein ligase HLTF; 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

EC 2.3.2.27

NP_033236.2

EC 2.3.2.27

XP_006535492.1

EC 2.3.2.27

XP_036018883.1

EC 2.3.2.27

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)

NM_001355097.1 → NP_001342026.1 DNA-dependent ATPase/E3 ubiquitin-protein ligase HLTF

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:472 → 1003

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

pfam08797
Location:60 → 153

HIRAN; HIRAN domain

cd16509
Location:752 → 795

RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins
NM_009210.3 → NP_033236.2 DNA-dependent ATPase/E3 ubiquitin-protein ligase HLTF

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:472 → 1003

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

pfam08797
Location:60 → 153

HIRAN; HIRAN domain

cd16509
Location:752 → 795

RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins

RNA

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
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

NC_000069.7 Reference GRCm39 C57BL/6J

Range

20111959..20172655

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (3) summary

COG0553
Location:329 → 860

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd16509
Location:609 → 652

RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins

cd18071
Location:97 → 495

DEXHc_HLTF1_SMARC3; DEXH-box helicase domain of HLTF1
XM_036162990.1 → XP_036018883.1 helicase-like transcription factor isoform X2

Conserved Domains (3) summary

COG0553
Location:129 → 660

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd16509
Location:409 → 452

RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins

cl28899
Location:129 → 295

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

RNA

XR_001783674.3 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_144959.2: Suppressed sequence

Description

NM_144959.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.