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

    Gene ID: 295568, updated on 9-Dec-2024

    Summary

    Official Symbol
    Hltfprovided by RGD
    Official Full Name
    helicase-like transcription factorprovided by RGD
    Primary source
    RGD:1309031
    See related
    EnsemblRapid: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 several processes, including mRNA transcription by RNA polymerase II; positive regulation of transcription by RNA polymerase II; and regulation of neurogenesis. Predicted to be located in nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in nucleus. Orthologous to human HLTF (helicase like transcription factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 528.3), Thymus (RPKM 185.6) and 9 other tissues See more
    Orthologs
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    Genomic context

    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

    Expression

    • 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

    General gene information

    Markers

    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 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 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

    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)

    NEW Try the new Transcript table

    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_001106478.1NP_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, ENSRNOT00000064828.5
      Conserved Domains (5) summary
      cd00046
      Location:443553
      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:724769
      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:243683
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:797915
      Helicase_C; Helicase conserved C-terminal domain
      pfam08797
      Location:60155
      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_006232175.5XP_006232237.1  helicase-like transcription factor isoform X1

      UniProtKB/TrEMBL
      A0A8I6AF43
      Related
      ENSRNOP00000092944.1, ENSRNOT00000106667.2
      Conserved Domains (6) summary
      smart00487
      Location:238316
      DEXDc; DEAD-like helicases superfamily
      cd00046
      Location:472597
      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:768813
      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:472727
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:841959
      Helicase_C; Helicase conserved C-terminal domain
      pfam08797
      Location:60155
      HIRAN; HIRAN domain
    2. XM_006232176.4XP_006232238.1  helicase-like transcription factor isoform X2

      UniProtKB/TrEMBL
      A0A0G2JVH5
      Related
      ENSRNOP00000069487.1, ENSRNOT00000090912.3
      Conserved Domains (5) summary
      cd00046
      Location:472582
      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:753798
      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:472712
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:826944
      Helicase_C; Helicase conserved C-terminal domain
      pfam08797
      Location:60155
      HIRAN; HIRAN domain
    3. XM_039102120.1XP_038958048.1  helicase-like transcription factor isoform X4

      Conserved Domains (4) summary
      COG0553
      Location:405956
      HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
      cd16509
      Location:705748
      RING-HC_HLTF; RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins
      pfam08797
      Location:291
      HIRAN; HIRAN domain
      cl28899
      Location:178591
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
    4. XM_006232177.4XP_006232239.1  helicase-like transcription factor isoform X3

      Conserved Domains (5) summary
      cd00046
      Location:443568
      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:739784
      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:243698
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:812930
      Helicase_C; Helicase conserved C-terminal domain
      pfam08797
      Location:60155
      HIRAN; HIRAN domain