Sde2 SDE2 telomere maintenance homolog [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sde2provided by RGD
Official Full Name: SDE2 telomere maintenance homologprovided by RGD
Primary source: RGD:1305572
See related: EnsemblRapid:ENSRNOG00000003247 AllianceGenome:RGD:1305572
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: RGD1305572
Summary: Predicted to enable damaged DNA binding activity and snoRNA binding activity. Predicted to be involved in several processes, including cellular response to UV; gene expression; and mitotic G1 DNA damage checkpoint signaling. Predicted to be located in several cellular components, including Golgi apparatus; mitochondrion; and nuclear speck. Predicted to be active in nucleus. Orthologous to human SDE2 (SDE2 telomere maintenance homolog). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 118.0), Spleen (RPKM 95.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q26

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (95110598..95126929)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (92578843..92595142)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (99136921..99153187)

Chromosome 13 - NC_086031.1 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?

Submit: New GeneRIF Correction

General gene information

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Markers

BQ205850 (e-PCR)
- UniSTS:261506

RH127324 (e-PCR)
- UniSTS:210634

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
enables damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables snoRNA binding	IEA Inferred from Electronic Annotation more info
enables snoRNA binding	ISO Inferred from Sequence Orthology more info
enables snoRNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in cellular response to UV	IEA Inferred from Electronic Annotation more info
involved_in cellular response to UV	ISO Inferred from Sequence Orthology more info
involved_in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IEA Inferred from Electronic Annotation more info
involved_in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	ISO Inferred from Sequence Orthology more info
involved_in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA cis splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in mRNA cis splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mitotic G1 DNA damage checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in mitotic G1 DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in protein processing	IEA Inferred from Electronic Annotation more info
involved_in protein processing	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in ribosome biogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology 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
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: UBL fusion protein SDE2

Names: UPF0667 protein C1orf55 homolog; protein SDE2 homolog; replication stress response regulator SDE2

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_001024970.3 → NP_001020141.2 UBL fusion protein SDE2

See identical proteins and their annotated locations for NP_001020141.2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/Swiss-Prot

Q5BJN8

UniProtKB/TrEMBL

A0A0G2KA69, A6JGH9

Related

ENSRNOP00000075283.2, ENSRNOT00000078263.3

Conserved Domains (2) summary

pfam13297
Location:382 → 441

Telomere_Sde2_2; Telomere stability C-terminal

cl00155
Location:69 → 146

UBQ; Ubiquitin-like proteins

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_086031.1 Reference GRCr8

Range

95110598..95126929

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090555.2 → XP_038946483.1 UBL fusion protein SDE2 isoform X1

UniProtKB/TrEMBL

A0A0G2KA69, A0A8L2Q245

Conserved Domains (2) summary

pfam13297
Location:393 → 452

Telomere_Sde2_2; Telomere stability C-terminal

cl28922
Location:69 → 157

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_039090557.2 → XP_038946485.1 UBL fusion protein SDE2 isoform X4

Conserved Domains (1) summary

cl28922
Location:69 → 157

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_039090558.2 → XP_038946486.1 UBL fusion protein SDE2 isoform X5

Conserved Domains (1) summary

cl28922
Location:69 → 146

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_039090554.2 → XP_038946482.1 UBL fusion protein SDE2 isoform X2

Related

ENSRNOP00000004350.7, ENSRNOT00000004350.8

Conserved Domains (1) summary

pfam13297
Location:361 → 420

Telomere_Sde2_2; Telomere stability C-terminal
XM_039090556.2 → XP_038946484.1 UBL fusion protein SDE2 isoform X3

Conserved Domains (1) summary

pfam13297
Location:265 → 324

Telomere_Sde2_2; Telomere stability C-terminal