Gene detail

Detailed information of aint_s0528.g24.t2 in Acropora intermedia

Genomic Location: sc0000528_pilon:285456...314536
NR annotation: XP_044177506.1, helicase SKI2W-like [Acropora millepora]
Species Acropora intermedia · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

aint_s0528.g24.t2

ATGGCGGACGAGAGAGAAGCTCAAGAGGAATGTGATCCGCTGGAATATGATTTCGATCTTCTGGAAGTTGGATGTACCGGGACTGTTGAGGTTATTCCACCATCAATCAACAAAACGTCAAAGAAAGAACTGAGCCCTTTAACAACACTACCTTCAGGGCTCCCACCTTTATTTCCTCCTGATTTGAAAACAGACTTGGAGAAATATCTCCTGGATCCCACGTCTTTGCCAATTCATGACTTTCATAAGACGCAAAGGTTTTGGCCTCGGGAAAGAGATTCAGAGAGTCTGTTCTATGCAGATGTCTGTCCAGTGCCAACAACGTTAAAGGTGGAGAGAAATCCAACAACTGGAGAGCTTCTTGGTTATAATGAGGTCATTTTGAAAGATACTGGTTCCACAGCCAAGAATTCTATGTCCATCTTGCGACAGCCAGGGCCGCTGTCGGCTTCAGTCAGGGGAGATTCTACCAATTACCCCTTTTTGCCAGGTGGCATGGACACTCAAGAAACAACAAAACCAGCCCTTGATTTTGATGGAGCACTAAACTTTGAGAACAATCTTTTCTCTCAACCACCAGGTTTTACCAGAGTGGTCTCATTTAATGACTCAAAAGCAGAGGAGGAAGTTAaaagagaaaaagaagacgatgaagaaaaaGGGAAGGATTCAAGTACATCACCACCTCAAGTTCTTGCTATGGCGGATATCATGGCTGGAACAACACTTGAAGATCTCGAGTACAGTGACGAAGAAAGTGAAGTAGACTCAGATGAAGATTATGTAAACCAGACCTCTGAAAAAGAAGAATATAATGTTGATCAGACAGATCCTGCAGAGGGAAATACAGAAGACAGTCTTGAAAATGTTTTAGTGAAGGAACAGGGCTCAGTTGTCAATAAATTCACGTCAGCTGCAACTGTTGCAGAAAAACCAGTGAAAGAGCAATGGGCTGTCATGATTAATGTCACAGAACCAGTGAAGGATTTTCACAAACGAGTTCCTGATATGGCGTACAAGttgaaggttcctggctggttgtttgtagatggtagGACAGTGTATACCTCGCCCATCAAAGCGTTATCCAACCAAAAGTTTCGCGAATTCAAGGACACTTTTGAGGATGTGGGTTTGCTAACTGGTGATGTCCAAATCAGACCTGAAGCGTCTTGCCTTATCATGACAACTGAAATCCTGCGTTCCATGTTGTACAATGGCTCTGACACAATCAGAGATGTGGAGTGGGTGATTTTTGATGAAGTACACTACATCAATGATGAAGAGAGGGGTGTCGTCTGGGAAGAGGTGCTGATCATGTTACCGGCTCAGGTCAAAATTATATTACTGTCGGCTACAGTCCCAAACACTCTGGAGTTTGCAGACTGGATTGGTCGCACCAAGAAAAAAAAGATCTACGTCATCAGCACGCCGAAGCGACCAGTTCCTCTCCAGCACTTCCTGTACACGGGCAACAGCAACAAAACAAGTAACGAACTATTTATGATCGTAGACGCTAACAGCAAGTTCCTGACGCGTGGTTACGATGCTACAGTAGAGGCGAAAAAAGAGCGGGAAGGAAAGGGAAAGGGCGCGTACGGTTCCAAGACTCATCAACCAGTCAACGTGAGGGAGGAGCGCAACGTTTGGCTTTCCTTGATTGAGATGCTGCGTAAGAAAGAAAAGCTACCTGTGGTGGCTTTTACCTTCTCAAGGAAGAGATGCGACGAAAATGCGGATCAGCTAAGCAGCCTTGATCTCACCACTTCCACGGAGAAGAGCTCAATTCATGTGTTCACTCAGAAGTGTGTGTCAAGACTCAAAGGAAATGATAGAAAGCTACCGCAAGTTTCCAGGATAAGGGAGCTCCTTAAACGCGGCCTCGGTGTCCATCATAGTGGAGTATTGCCCATAATAAAAGAGATGGTGGAGATGTTGTTTGGACGAGGATTGGTGAAGATTCTGTTTGCTACAGAGACGTTTGCTATGGGAGTCAACATGCCCGCCAGAACAGTGGTGTTTGATTCAATAAGGAAACATGATGGAACTGTCTTTCGAGATCTTTTACCCGGAGAGTACATCCAAATGGCTGGCCGCGCGGGACGAAGAGGACTGGACCCGACCGGAACTGTGATCCTGCTTTGCAAAGCAAATGTCCCTCTGATGGCTGATCTACACAAAATGATGCTGGGCAAACCAACACAATTGGTTTCCAGATTTCGTCTCACTTACTCCATGATCCTGAATCTTTTGCGAGTTGAGGAGTTGCGCGTGGAAGACATGATGAAAAGGAGTTTTGCCGAGTTTCATATGCAAAAGGATGCACAAGAGAGAAAACGCGAAATGGAAGAATTAGAACAAAAGCTGCAAAATGTCAAGGAACTGGACTGTACGTTTTGCTCGGAGGATTTGAAATTATACTTCAAAGGTTGCAGAGAGCTGTCGGAATTAACACGAATTGTTCAGGCTGCGATTCTCTCATCTGCTCAGGGTCAGCGGGCTCTCTCTCCAGGGCGTGTTGTCACCATAAATACTTCTGAACACAGAAACGCCCTCGCTGTGATATTGCAAGCGGAAAATCCCCCGAACCAGGGTTACCCAACCATGCATTCTCGGCCAGTTTCCAGTCCCAAAGAAAGGCACTTCCTCGTCCTCGTCATATGTGACGCACAAGAGCAAACACCTGGTTCAGGTGACGAAGATTCAGTTTCCAAGCCAGGCGTGCCTTCAGCCGTGTCACAAGAGTGA

Transcript

aint_s0528.g24.t2

TTTACCCAGCTGGAACCCGGTCAAGATGGCGGACGAGAGAGAAGCTCAAGAGGAATGTGATCCGCTGGAATATGATTTCGATCTTCTGGAAGTTGGATGTACCGGGACTGTTGAGGTTATTCCACCATCAATCAACAAAACGTCAAAGAAAGAACTGAGCCCTTTAACAACACTACCTTCAGGGCTCCCACCTTTATTTCCTCCTGATTTGAAAACAGACTTGGAGAAATATCTCCTGGATCCCACGTCTTTGCCAATTCATGACTTTCATAAGACGCAAAGGTTTTGGCCTCGGGAAAGAGATTCAGAGAGTCTGTTCTATGCAGATGTCTGTCCAGTGCCAACAACGTTAAAGGTGGAGAGAAATCCAACAACTGGAGAGCTTCTTGGTTATAATGAGGTCATTTTGAAAGATACTGGTTCCACAGCCAAGAATTCTATGTCCATCTTGCGACAGCCAGGGCCGCTGTCGGCTTCAGTCAGGGGAGATTCTACCAATTACCCCTTTTTGCCAGGTGGCATGGACACTCAAGAAACAACAAAACCAGCCCTTGATTTTGATGGAGCACTAAACTTTGAGAACAATCTTTTCTCTCAACCACCAGGTTTTACCAGAGTGGTCTCATTTAATGACTCAAAAGCAGAGGAGGAAGTTAaaagagaaaaagaagacgatgaagaaaaaGGGAAGGATTCAAGTACATCACCACCTCAAGTTCTTGCTATGGCGGATATCATGGCTGGAACAACACTTGAAGATCTCGAGTACAGTGACGAAGAAAGTGAAGTAGACTCAGATGAAGATTATGTAAACCAGACCTCTGAAAAAGAAGAATATAATGTTGATCAGACAGATCCTGCAGAGGGAAATACAGAAGACAGTCTTGAAAATGTTTTAGTGAAGGAACAGGGCTCAGTTGTCAATAAATTCACGTCAGCTGCAACTGTTGCAGAAAAACCAGTGAAAGAGCAATGGGCTGTCATGATTAATGTCACAGAACCAGTGAAGGATTTTCACAAACGAGTTCCTGATATGGCGTACAAGttgaaggttcctggctggttgtttgtagatggtagGACAGTGTATACCTCGCCCATCAAAGCGTTATCCAACCAAAAGTTTCGCGAATTCAAGGACACTTTTGAGGATGTGGGTTTGCTAACTGGTGATGTCCAAATCAGACCTGAAGCGTCTTGCCTTATCATGACAACTGAAATCCTGCGTTCCATGTTGTACAATGGCTCTGACACAATCAGAGATGTGGAGTGGGTGATTTTTGATGAAGTACACTACATCAATGATGAAGAGAGGGGTGTCGTCTGGGAAGAGGTGCTGATCATGTTACCGGCTCAGGTCAAAATTATATTACTGTCGGCTACAGTCCCAAACACTCTGGAGTTTGCAGACTGGATTGGTCGCACCAAGAAAAAAAAGATCTACGTCATCAGCACGCCGAAGCGACCAGTTCCTCTCCAGCACTTCCTGTACACGGGCAACAGCAACAAAACAAGTAACGAACTATTTATGATCGTAGACGCTAACAGCAAGTTCCTGACGCGTGGTTACGATGCTACAGTAGAGGCGAAAAAAGAGCGGGAAGGAAAGGGAAAGGGCGCGTACGGTTCCAAGACTCATCAACCAGTCAACGTGAGGGAGGAGCGCAACGTTTGGCTTTCCTTGATTGAGATGCTGCGTAAGAAAGAAAAGCTACCTGTGGTGGCTTTTACCTTCTCAAGGAAGAGATGCGACGAAAATGCGGATCAGCTAAGCAGCCTTGATCTCACCACTTCCACGGAGAAGAGCTCAATTCATGTGTTCACTCAGAAGTGTGTGTCAAGACTCAAAGGAAATGATAGAAAGCTACCGCAAGTTTCCAGGATAAGGGAGCTCCTTAAACGCGGCCTCGGTGTCCATCATAGTGGAGTATTGCCCATAATAAAAGAGATGGTGGAGATGTTGTTTGGACGAGGATTGGTGAAGATTCTGTTTGCTACAGAGACGTTTGCTATGGGAGTCAACATGCCCGCCAGAACAGTGGTGTTTGATTCAATAAGGAAACATGATGGAACTGTCTTTCGAGATCTTTTACCCGGAGAGTACATCCAAATGGCTGGCCGCGCGGGACGAAGAGGACTGGACCCGACCGGAACTGTGATCCTGCTTTGCAAAGCAAATGTCCCTCTGATGGCTGATCTACACAAAATGATGCTGGGCAAACCAACACAATTGGTTTCCAGATTTCGTCTCACTTACTCCATGATCCTGAATCTTTTGCGAGTTGAGGAGTTGCGCGTGGAAGACATGATGAAAAGGAGTTTTGCCGAGTTTCATATGCAAAAGGATGCACAAGAGAGAAAACGCGAAATGGAAGAATTAGAACAAAAGCTGCAAAATGTCAAGGAACTGGACTGTACGTTTTGCTCGGAGGATTTGAAATTATACTTCAAAGGTTGCAGAGAGCTGTCGGAATTAACACGAATTGTTCAGGCTGCGATTCTCTCATCTGCTCAGGGTCAGCGGGCTCTCTCTCCAGGGCGTGTTGTCACCATAAATACTTCTGAACACAGAAACGCCCTCGCTGTGATATTGCAAGCGGAAAATCCCCCGAACCAGGGTTACCCAACCATGCATTCTCGGCCAGTTTCCAGTCCCAAAGAAAGGCACTTCCTCGTCCTCGTCATATGTGACGCACAAGAGCAAACACCTGGTTCAGGTGACGAAGATTCAGTTTCCAAGCCAGGCGTGCCTTCAGCCGTGTCACAAGAGTGAAGGGAACTGAAATCAGCGCTATTTCTGTTCGCCAACTGAAGCTGGACACAAGCAAAATCATCGATGATCACAAGAAAAGAATGCTGCCCAGATTCAGAAACGATCCACCGGGAAGAACGACAGTAACAGCTGAACAAGAACTGCTGCGATTGTCCGAGGCAAATCCAGAGGGACTGGACAAAATGGATCCGGTCAAAGATTTCAACATCCGAGATATCGACATGGTGACAACAATCGCACGAAAGCAAAGCCTTGAAGAGAGTATAACCAGCTTCAAATGTTTAGACTGTCCTAAGTTTACGGGACATTTTGAAGCTATCGCGCACCAGATGAGGCTCCGTGAGCACGTGACTTCGCTCAGGTATTTGTTGTCGGATGAAAGTCTGCAACACACAGAGGAGCTTCGACAGAGAATTCAGGTGCTACAGAAATTGCGTTATGTGGATGCTAACAATGCTGTGCAGCTTAAAGGAAGAGTAGCATGTGAGATAAACAACCACGAACTCATTATTACAGAGCTTGTGTTTGAAAATGCTTTCACCGATCTACATCCTACAGAAATTGTTGCTTTGTTGTCCTGTTTCGTCTTCCAGCAGCGTCGTTGCAGCGAACCAAAACTAACAAAGACCCTAGAGGAGGGCAAGAAGCGTATCTTATCCATGGCTGAGGAGATCGCCTACCTTCAGTCAGATTGCGGTCTAGTCACATCCGTTGAAGAGTTTAAAGAGCAGTACAAGTTTGGTTTGGTTGAAGCAGTGTTTGAGTGGGCGCGCGGTATGCCTTTCTCCGAAATCACCAATCTAACAGATGTCCAGGAAGGAATTATCGTTCGATGTATTCAGCGATTGGACGAGACGTGTCGTGACGTCAGGAATGCTGCTCGTGTTATTGGAGATCCAAAACTTGGCGAGAAGATGGAAGAAGCTTCTGCCATGATTAAAAGAGATATAGTATTCGCTGCGAGCCTGTACACACAGTAAAACTTCATTCAACACATAGTGCAGGACATGCCTTGGCCTGTACAAGGCTATGGGTATACTGCGGAACACAGGAAAAACATACTGACAGGAGGTCAAGAAGCTAACGTACACTCTTGAGCTACACAGAGACCAATGTCTGGAACTGCGGAAATGAACTAGTTCAAACAGAATTGAGTTCGGATGTCTGCAATGATTGTATGTGATCTTTTTAGGTCGGTTTTTTGTTTTAGCGAATGGGGACTGCATTTACTGGTCTATTTTAGAGTCATTGGGTCCAACATATTTTTAGGAGAACGCTTTCTTTTATCGTCTTTTTGAGAGGGTTCTCGCCGTTTTCCCCAAGAGTACAATATTCGATGCCATTTGTTTTCAAGGTTTCGATGGACTGACTGACATTTATCCGCAAATTTCATGGTCTAAATGGCTAGCCTTATTAACCACAGGTCTCCCGTCAATAACATACGCTCGTTCTACGCGTGCGTGGTCGACCGAAATATTCCTCGTAAAGTTGGATCAATTTCCGACCATTTTTCCAAAGTATCTTTTACCAATGTGATTGATACTAGTCATGAAAAGATAAGAAAGCTGTGCGGTAATGTGTCTTCTAGGAACAGATGCTGCAATTTGATCAAATACAAAGTCTTTGCACTGATTTATGATAATGTCTAGTGCATATTTTAAACAAAAAAAGAACAGGAAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6NZR5	Superkiller complex protein 2 OS=Mus musculus OX=10090 GN=Skic2 PE=2 SV=1
Q15477	Superkiller complex protein 2 OS=Homo sapiens OX=9606 GN=SKIC2 PE=1 SV=3
O59801	Putative ATP-dependent RNA helicase C550.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPCC550.03c PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001220 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21408 all species →	MTR4-like_stalk	Exosome RNA helicase MTR4-like, stalk	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan
PF17911 all species →	Ski2_N	Ski2 N-terminal region	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR016438 all species →	Family	ATP-dependent RNA helicase SKI2-like	Interproscan
IPR048392 all species →	Domain	Exosome RNA helicase MTR4-like, stalk	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR050699 all species →	Family	RNA/DNA Helicase	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan
IPR040801 all species →	Domain	Ski2, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12131 all species →	ATP-DEPENDENT RNA AND DNA HELICASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0006401 all species →	Biological Process	RNA catabolic process	Interproscan
GO:0055087 all species →	Cellular Component	Ski complex	Interproscan
GO:0070478 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for aint_s0528.g24.t2.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora intermedia tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora intermedia, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →