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

Summary

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

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_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circadian Prl transcription depended on an interaction between the pituitary-specific transcription factor, PIT-1, and the helicase-like transcription factor (HLTF), a SWI/SNF chromatin remodeler.
Title: Chromatin remodeling as a mechanism for circadian prolactin transcription: rhythmic NONO and SFPQ recruitment to HLTF.

Submit: New GeneRIF Correction

General gene information

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Markers

RH140388 (e-PCR)
- UniSTS:222464

RH127313 (e-PCR)
- UniSTS:210623

AU047370 (e-PCR)
- UniSTS:110574

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

EC 2.3.2.27

XP_006232237.1

EC 2.3.2.27

XP_006232238.1

EC 2.3.2.27

XP_006232239.1

EC 2.3.2.27

XP_038958048.1

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_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

NC_086020.1 Reference GRCr8

Range

104478725..104538531

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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