Gene detail

Detailed information of evm.model.HiC_scaffold_2.257 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_2:3327324...3343459
NR annotation: XP_012555972.2, SWI/SNF complex subunit SMARCC2 [Hydra vulgaris]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_2.257

ATGGCTGTTAGAAAGAAAGATGGAGGAACGAACTGGAAGTATTTTGAATCTCAAGaaaccatcgaactgtttgaacCAGTCAGGCAATATCTGCTGAAGAACCACAAAAAATATGTTCAAGCAGATCCTCCAACAAATAAAACATTGTCTCATCTGACAGGACAGCTTATTCAGTTTCAAGAGGAAGCCTTTGGAAAGAATGTAAGCAAACCAGCATTGACAAGGCTGCCAatgaAACAGCTGTTAGATTTTTCATTTGGTGGCTCTCTCTGTCAAATCATTGCAGCGTCGTACAAATTTAAAGTTGATCAAGGATGGAGAAGGTTTGATTTTCAGTCTCCATCTAGAATGGATCGAAATGTTGAACTGTTTATGACGATTGAAAAAACATTACGAGAGAACAAATTACTGGAACGACCCAAGGTATATCTACTGCCAGACATTGAAACAAAACTTGCTAATAAACTCCGAGAGATTGTTAAAAGACACCAGGGTACCTTGGTAGACGCAAAAGATAAAGCAACACACATCGTCCATTCCACTCCTATGCCATGTCCTGATGAGGATTGGCTAAGGCCTATATCAAGAAAGGATAAACAAGTTCTAGTACACTGGTGGTACCATCCTGAtagctACGATTCCTGGCTTCCTTTATCTGAAGTATCACAAGAACCAGAACCAGCCCCAGAAAGACAAAAACCATGGGAGGTTAACGGCAGATGGCTGTTAGACTTAGAGATATTCAACGAATGGATGAATGAAGAAGATTATGAAATGGAAAACACGGAGGTTAgaaaaacaagaagaaaagtcATTAAAGGGAAATCATGCTCTGAAGATGTAAGGggagattttattttatttgatatGAGAACGTTCTGCGAGAAAAGAAAATCTTCGCCATCACCATCTCCCGAACCTGCtaaaaggaagaagaagggaTCGAAGAAAAAGGATGAGGAAAAATCAGAAAGAGACGAAGATTTGTACTTTGATTATCTTCTTAATTCGGTTGATTATTTAGTTTCAAATACAAAAGTATTACACATAGATAATGTGGGATGTATACTGTTGATTCTCGTTAATGCAGTTTGTGGGAAGACTCAtaaccttcctcccactcttttggaaacagcaTCTTACAACTACAGCAACAAAAAGCTGTCTCCTCAAACTACTCTAAAGCAAACAGCAACTAGTACAACGTCGGGAAAACAGTCGGAGTCTAAAAAGATCAATGAAACTGTCAATCGAGAACCCGAGATCCCACATGATGATAATCTACCAGAACAAACACGACATATCATTATACCAAGCTATGCTGCATGGTTTGATTACAACAGCATTCACGCAATTGAGCGAAGAGCATTACCAGAatttttcaatggaaaaaacaaatcaaaaacagcAGAAGTATACTTTGCATATAGGAACTTTATGATTGATACTTATCGACTTAACCCAACGGAATACTTCACTGCGACAGCATGTAGAAGAAACTTAGCTGGGGATGTCTGTGCTATTGTAAGgGTCCATGCCTTCTTAGAGCAATGGGGCCTCGTTAACTATCAAGTAGATGCAGACAACAGACCTTTGCCAATGGGACCTCCTCCTACGTCGCATTTCCATGTTCTCTGTGATACGCCATCTGGACTTCAACCGCTTGTTGGATCAAAACCACCGATGTCTGCTGCCCAGCAACTGATCAACCTTGCTGATAAAGAAAACACAAGCAACAAGACCAACGAAGGAAATAATTTTGGGCTTCGAACAGATGTTTATTTGACTAAAAAACAGATCAAGAGTAAATCTGCAGCCTACAAAGAATGGACGGATCAAGAAACCTTACTCTTACTCGAGGGACTTGAGCTTCACAAAGATGATTGGAACAAAGTGGCAGAGCATGTTGGTACACGAATGCAGGATGAATGTATTCTTCAGTTTCTACGTCTTCCTGTTGAAGATCCTTATCTCGAAGATGGTGGCAGCTCGCTAGGTGTTCTGGGGCATCAGCCGATACCGTTTAGCCAAGCTGGTAATCCTGTTATGTCTACAGTGGCATTCCTTGCCTCTATTGTTGAACCAAGGGTAGCAAGTGCAGCAGCCAAGGCAGCAATAGagGAATTTGCTCGTCTCAAAGAAGAAATCCCAGACTCACTAATCGATGCACATTTATCACATGGAAAACAGGAGGCAGAAAAGGCAGAGACCCAAAGCGATGGAAAAACTGACGAGAAGGAAAGCGCCGATAAAGAAAAGAACGATGCAGATGGTGAAGAGAAGAAACAAGAAGAGAAAAAACCAAAAGAGATATCGCCAGAATTAGCTGAAAGAGCTGATGAATTACTGAAGAAAAGAGCAGAATTAAAGGAAGGAAATATTAAATCAGCCGCCTCAGTTGCACTGGCTGCTGCTGCTGTCAAAGCTAAGCATTTGGCGCAAGTAGAAGAAAGGAAAATCAAGAGCCTTGTGGCACTCCTTGTTGAAACTCAGATGAAGAAATTGGAGATCAAACTTCGACATTTTGAAGAACTGGAAACTATTATGGAAAGAGAAAGAGAATTGCTTGAACAACAAAGACAGCAACTATTAGCTGAAAGACAACAGTTTTTCATGGAGCAATTACAACAATCAGAAGCAAAGTCTAAAAACGCAGATGACACATTGACTCAGCCTAAAGCTCCGGCTGCTACATTAGCCAATGTAACTGCAACAGCATCGTCAGTCACTGAGCCGACCTCGTTGCAATCATCGCAGAAAGGAACCTTATCGTCCACAGAGTCAGTCACACCCAAACCAGCCACTCCGAAAGAGGATTCGGTTGATACGGAGCAGCTTCAATCTCATCCATCGTCGTCATCTGCGGAGGTACTGAAAAATGCGCCAACTTCAGTTACGCAAGCGTTTGCTGGGGCTGAAAGAACGAGCGATCAAACCATGGCACAAACCCAGCCGCAGTCGAAAGCCCAAGAAACGATGATGCAGAACCTGGTGATGTCTCAAGCAAGGCAACCCCATGTTCGCGGCAAACGCTATGAGCGACCAACCCCAAACTTGATGCCACAAGATGGCAAACCAGCCGCTGTCAGTCAGATGCAGATGCCGCAGTTTTCTCAAGCACCTAACATGCAAACTGCTCAACGGCTACCACAGCAGCGAAGATCTCAGATGCAACCTCAAGGATACCCCAACCCGAATGCGATGGTCCCTGGTGCGATGACTGGTAACCAACAAGGCAACAACCCTTCCGTTCAGTATTCATATCCCGGGGCATTCCAAGGACAACAGATGGGAATGATGTCACAAGCTATGCAACCCCCTGCTTACGGTAATAACCCAATGATGCAGCAAGGGATGAACATGATGCAGCAAGGGGGTCCTCCCATGAGTATGGGACCAGGACAATACCAACAAGGACAATTTGGACCTTCCTTTCCTCATATGTAA

Transcript

evm.model.HiC_scaffold_2.257

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8TAQ2	SWI/SNF complex subunit SMARCC2 OS=Homo sapiens OX=9606 GN=SMARCC2 PE=1 SV=1
P97496	SWI/SNF complex subunit SMARCC1 OS=Mus musculus OX=10090 GN=Smarcc1 PE=1 SV=2
Q6PDG5	SWI/SNF complex subunit SMARCC2 OS=Mus musculus OX=10090 GN=Smarcc2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003834 (this species only) · gene tree & orthology
Transcription factor family	MYB · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00249 all species →	Myb_DNA-binding	Myb-like DNA-binding domain	Domain	Interproscan
PF16496 all species →	SWIRM-assoc_2	SWIRM-associated domain at the N-terminal	Family	Interproscan
PF16498 all species →	SWIRM-assoc_3	SWIRM-associated domain at the C-terminal	Family	Interproscan
PF16495 all species →	SWIRM-assoc_1	SWIRM-associated region 1	Family	Interproscan
PF04433 all species →	SWIRM	SWIRM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001005 all species →	Domain	SANT/Myb domain	Interproscan
IPR049898 all species →	Domain	MarR-like, BRCT and chromo domains module	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR032450 all species →	Domain	SMARCC, N-terminal	Interproscan
IPR032448 all species →	Domain	SMARCC, SWIRM-associated domain	Interproscan
IPR007526 all species →	Domain	SWIRM domain	Interproscan
IPR032451 all species →	Domain	SMARCC, C-terminal	Interproscan
IPR017884 all species →	Domain	SANT domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12802 all species →	SWI/SNF COMPLEX-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0016514 all species →	Cellular Component	SWI/SNF complex	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:0045893 all species →	Biological Process	positive regulation of DNA-templated transcription	Interproscan
GO:0005515 all species →	Molecular Function	protein 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K11649	SMARCC; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C	-	Chromosome and associated proteins	ko03036	deepkoala

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 Chrysaora quinquecirrha 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 Chrysaora quinquecirrha, 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 →