Setx senataxin [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Setxprovided by RGD
Official Full Name: senataxinprovided by RGD
Primary source: RGD:1565575
See related: Ensembl:ENSRNOG00000013491 AllianceGenome:RGD:1565575
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1565575
Summary: Predicted to enable RNA binding activity; identical protein binding activity; and transcription termination site sequence-specific DNA binding activity. Predicted to be involved in several processes, including intracellular signal transduction; nucleic acid metabolic process; and positive regulation of RNA metabolic process. Predicted to act upstream of or within circadian rhythm. Predicted to be located in several cellular components, including growth cone; intercellular bridge; and nuclear lumen. Predicted to be active in nuclear body. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2. Orthologous to human SETX (senataxin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 501.6), Spleen (RPKM 376.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3p12

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (32825771..32878740)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (12428091..12480801)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (7680430..7731815)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables transcription termination site sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables transcription termination site sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA-templated transcription termination	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to oxidative stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in mRNA splice site recognition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription initiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of termination of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled	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 termination of RNA polymerase II transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within termination of RNA polymerase II transcription	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in growth cone	ISO Inferred from Sequence Orthology more info
located_in intercellular bridge	IEA Inferred from Electronic Annotation more info
located_in intercellular bridge	ISO Inferred from Sequence Orthology more info
is_active_in nuclear body	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear chromosome	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: probable helicase senataxin

Names: DEAxQ-box helicase; tRNA splicing endonuclease regulator 1

NP_001414209.1

EC 3.6.1.-

XP_006233948.1

EC 3.6.1.-

XP_006233949.1

EC 3.6.1.-

XP_038962080.1

EC 3.6.1.-

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)

NM_001427280.2 → NP_001414209.1 probable helicase senataxin

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

D4AEB3

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_086021.1 Reference GRCr8

Range

32825771..32878740

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006233887.5 → XP_006233949.1 probable helicase senataxin isoform X1

See identical proteins and their annotated locations for XP_006233949.1

UniProtKB/TrEMBL

A0A8I5ZVF7, A0A8I5ZYQ6

Related

ENSRNOP00000082851.1

Conserved Domains (4) summary

pfam12726
Location:37 → 356

SEN1_N; SEN1 N terminal

pfam13086
Location:1910 → 2195

AAA_11; AAA domain

pfam13087
Location:2202 → 2456

AAA_12; AAA domain

pfam13245
Location:1934 → 1997

AAA_19; Part of AAA domain
XM_039106152.2 → XP_038962080.1 probable helicase senataxin isoform X2

UniProtKB/TrEMBL

A0A8I5ZVF7

Conserved Domains (3) summary

COG1112
Location:1641 → 2256

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

cd18042
Location:1911 → 2236

DEXXQc_SETX; DEXXQ-box helicase domain of SETX

pfam12726
Location:37 → 334

SEN1_N; SEN1 N terminal
XM_006233886.5 → XP_006233948.1 probable helicase senataxin isoform X1

See identical proteins and their annotated locations for XP_006233948.1

UniProtKB/TrEMBL

A0A8I5ZVF7, A0A8I5ZYQ6

Related

ENSRNOP00000083466.1

Conserved Domains (4) summary

pfam12726
Location:37 → 356

SEN1_N; SEN1 N terminal

pfam13086
Location:1910 → 2195

AAA_11; AAA domain

pfam13087
Location:2202 → 2456

AAA_12; AAA domain

pfam13245
Location:1934 → 1997

AAA_19; Part of AAA domain