Skic2 SKI2 subunit of superkiller complex [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Skic2provided by RGD
Official Full Name: SKI2 subunit of superkiller complexprovided by RGD
Primary source: RGD:1303059
See related: Ensembl:ENSRNOG00000000421 AllianceGenome:RGD:1303059
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: Skiv2l
Summary: Predicted to enable RNA helicase activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay. Predicted to be part of Ski complex. Human ortholog(s) of this gene implicated in trichohepatoenteric syndrome 2. Orthologous to human SKIV2L (Ski2 like RNA helicase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 117.0), Kidney (RPKM 104.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (3987130..3997887)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (3982494..3993261)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4519457..4530177, complement)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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 3'-5' RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	ISO Inferred from Sequence Orthology more info
involved_in rescue of stalled ribosome	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Ski complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Ski complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: superkiller complex protein 2

Names: SKI2 homolog, superkiller viralicidic activity 2-like; Ski2 like RNA helicase; helicase SKI2W; superkiller viralicidic activity 2-like

NP_998724.1

EC 3.6.4.13

XP_006255985.1

EC 3.6.4.13

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_213559.2 → NP_998724.1 superkiller complex protein 2

See identical proteins and their annotated locations for NP_998724.1

Status: VALIDATED

Source sequence(s)

BX883045

UniProtKB/TrEMBL

A6KTK7, F1LP39, Q6MG76

Conserved Domains (6) summary

smart00490
Location:618 → 702

HELICc; helicase superfamily c-terminal domain

COG4581
Location:285 → 1239

Dob10; Superfamily II RNA helicase [Replication, recombination and repair]

pfam00270
Location:309 → 456

DEAD; DEAD/DEAH box helicase

pfam08148
Location:1067 → 1233

DSHCT; DSHCT (NUC185) domain

pfam13234
Location:759 → 1037

rRNA_proc-arch; rRNA-processing arch domain

pfam15345
Location:216 → 274

TMEM51; Transmembrane protein 51

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_086038.1 Reference GRCr8

Range

3987130..3997887

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255923.4 → XP_006255985.1 superkiller complex protein 2 isoform X1

UniProtKB/TrEMBL

A6KTK7

Related

ENSRNOP00000000481.5

Conserved Domains (6) summary

smart00490
Location:621 → 705

HELICc; helicase superfamily c-terminal domain

COG4581
Location:288 → 1242

Dob10; Superfamily II RNA helicase [Replication, recombination and repair]

pfam00270
Location:312 → 459

DEAD; DEAD/DEAH box helicase

pfam08148
Location:1070 → 1236

DSHCT; DSHCT (NUC185) domain

pfam13234
Location:762 → 1040

rRNA_proc-arch; rRNA-processing arch domain

pfam15345
Location:219 → 277

TMEM51; Transmembrane protein 51