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Hltf helicase-like transcription factor [ Rattus norvegicus (Norway rat) ]

Gene ID: 295568, updated on 2-May-2024

Summary

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Official Symbol
Hltfprovided by RGD
Official Full Name
helicase-like transcription factorprovided by RGD
Primary source
RGD:1309031
See related
Ensembl:ENSRNOG00000000082 AllianceGenome:RGD:1309031
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Snf2l3; Smarca3
Summary
Predicted to enable ATP-dependent activity, acting on DNA; ubiquitin protein ligase activity; and ubiquitin protein ligase binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Orthologous to human HLTF (helicase like transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Heart (RPKM 528.3), Thymus (RPKM 185.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Hltf in Genome Data Viewer
Location:
2q24
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (104478725..104538531)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (102549724..102609492)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (104854571..104914338)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene ceruloplasmin Neighboring gene HPS3, biogenesis of lysosomal organelles complex 2 subunit 1 Neighboring gene uncharacterized LOC134485607 Neighboring gene glycogenin 1 Neighboring gene eukaryotic translation initiation factor 4 gamma 1, pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Biochemical characterisation of the SWI/SNF family member HLTF. MacKay C, et al. Biochem Biophys Res Commun, 2009 Dec 11. PMID 19723507
  2. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling. Achar YJ, et al. Nucleic Acids Res, 2015 Dec 2. PMID 26350214, Free PMC Article
  3. Molecular cloning and characterization of P113, a mouse SNF2/SWI2-related transcription factor. Zhang Q, et al. Gene, 1997 Nov 20. PMID 9427542
  4. Chromatin remodeling as a mechanism for circadian prolactin transcription: rhythmic NONO and SFPQ recruitment to HLTF. Guillaumond F, et al. FASEB J, 2011 Aug. PMID 21507896
  5. SHPRH and HLTF act in a damage-specific manner to coordinate different forms of postreplication repair and prevent mutagenesis. Lin JR, et al. Mol Cell, 2011 Apr 22. PMID 21396873, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
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 ISO
Inferred from Sequence Orthology
more info
  
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
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 ubiquitin protein ligase activity ISO
Inferred from Sequence Orthology
more info
  
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
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 mRNA transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of neurogenesis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
helicase-like transcription factor
Names
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3
NP_001099948.1
XP_006232237.1
XP_006232238.1
XP_006232239.1
XP_038958048.1

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_001106478.1 → NP_001099948.1  helicase-like transcription factor

    See identical proteins and their annotated locations for NP_001099948.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473961
    UniProtKB/TrEMBL
    A6IHC7, D3ZMQ9
    Related
    ENSRNOP00000060341.1, ENSRNOT00000064828.4
    Conserved Domains (5) summary
    cd00046
    Location:443 → 553
    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:724 → 769
    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:243 → 683
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:797 → 915
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60 → 155
    HIRAN; HIRAN domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    104478725..104538531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006232175.5 → XP_006232237.1  helicase-like transcription factor isoform X1

    UniProtKB/TrEMBL
    A0A8I6AF43
    Related
    ENSRNOP00000092944.1
    Conserved Domains (6) summary
    smart00487
    Location:238 → 316
    DEXDc; DEAD-like helicases superfamily
    cd00046
    Location:472 → 597
    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:768 → 813
    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:472 → 727
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:841 → 959
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60 → 155
    HIRAN; HIRAN domain

  2. XM_006232176.4 → XP_006232238.1  helicase-like transcription factor isoform X2

    UniProtKB/TrEMBL
    A0A0G2JVH5
    Related
    ENSRNOP00000069487.1
    Conserved Domains (5) summary
    cd00046
    Location:472 → 582
    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:753 → 798
    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:472 → 712
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:826 → 944
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60 → 155
    HIRAN; HIRAN domain

  3. XM_039102120.1 → XP_038958048.1  helicase-like transcription factor isoform X4

    Conserved Domains (4) summary
    COG0553
    Location:405 → 956
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd16509
    Location:705 → 748
    RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins
    pfam08797
    Location:2 → 91
    HIRAN; HIRAN domain
    cl28899
    Location:178 → 591
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

  4. XM_006232177.4 → XP_006232239.1  helicase-like transcription factor isoform X3

    Conserved Domains (5) summary
    cd00046
    Location:443 → 568
    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:739 → 784
    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:243 → 698
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:812 → 930
    Helicase_C; Helicase conserved C-terminal domain
    pfam08797
    Location:60 → 155
    HIRAN; HIRAN domain
Nucleotide Protein Strain
Heading Accession and Version

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