Gene detail

Detailed information of evm.model.HiC_scaffold_248.6 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_248:47169...51126
NR annotation: VZI13621.1, unnamed protein product [Spirometra erinaceieuropaei]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_248.6

ATGAATGATTCAGAACAAGCACAAGCACCAGCACCAACTTCATCTGCTAATCCTACTAACGAACCAGCTCCAGCAAATCCTTCTCCTGCTGAGATTCCTGTCGCTGCCCTGAGTCTGAAATTACCACCTTTTTGGCCTAATGACCCTACAATTTGGTTCGCACAAGTCGAAGCTCAGTTTCTTACACGAAATATCACTTCTCAGCGTTCGAAATTTGCTCATGTCATAGCTAATTTACCTCCAGAAATCGCTCAAGAAATACGGGACATTATAGTCAGCCCACCTGAGGAAAACCGATTTGATTACCTAAAAACTGAGTTGATCAAACGTACATCAGCTTCTGAACAGAAACGCCTTCACCAGTTATTAATTTCGGAAGAACTCGGTGATCGAAAACCTACTCAGCTTTTACGTAGGATGCGTCAGCTTCTTGGCGACCATCATTTAGAAGACCGAATTTTGCGTCAACTCTTCTTACAGCGCCTTCCTATGAATGCACAGCTTATTCTCGCTTCCACCGCTGAAACTGTCTCGGTTGACCAGCTAGCCACGATCGCTGATAAGATTCTTGAAGTTGCTTTACCAGCACCTGTCATATCCAGCTTGCCACCAACCACATCTTCCCCACCAACCTCTGAAGTTCAAGAGTTTCGTTCTCAATTAGAAGCACTCACTTCTCAAGTCCAGGCTTTGGTTAATCATGTTGGTTTGCAAAACCCACCACGCAACAGAGGAAAACATCCAAGCCAGCGACTAGAGGCGACACGTCCCACTGGCTCAAACACTCCTAGTCGCCTATTTTATGTAACCGATCGTATCACAGGTACACGTTTTTTGGTTGATACAGGCGCCGATGTCAGTGTAATTCCTCCTTCTCGCTCTGCTAAACAACACGTTTCCTCACTTACCTTGCAAGCCGTGAATCGCTCCTCCATTGCCACCTACGGAGAAAAATCTTTGACTTTGGATATTGGACTTCGCCGTACGTTCAGATGGATTTTCATTCTTGCAGATATTCCTACCCCTATTCTTGGTGCAGATTTTCTCGCACATTTTAACCTCACTGTAGATATTCGTCAACGCAAACTAATCGACTCTACTACGAAATTAACCATTCATGGAATTCAATCATCAGATTCGTCACCTCAACTCATGTTCAGCATTCCTGACTCTGATAGGCCTAATCAATACCATGATTTAATTAAACAGTTTCCTGATCTCACTCGTACTACTTACGAAGAAACTGCAGTTAAACATTCACTAGGCATCATTCGTCAATCTGAAAGCAGTTGGTCCTCTCCATTGCACATGGTTCCTAAGAAATCAGGTGACTGGCGTCCTTGCGGAGATTATCGTGCACTGAATAAAGTTACCATACCTGACAGATATCCTATCCCACATATTCAAGACTTTAGCTCTTCATTGCATGGCAAAACTGTATTCTCCAAGATAGATTTAGTTCGTGCATACCACCAAATTCCGGTAGAGCCTAGTGATATACCCAAAACTGCCATAATAACCCCTTTTGGTCTGTTTGAATTCGTCCGTATGCCTTTTGGTCTTCGAAATGCTGCACAAACCTTCCAACGGTTTATCGATGAAGTTTTACGTGGTCTGGATTTCGTTTATGCTTATATTGACGATTTATTAATTGCTAGTTCATCCGAATCTGAACATCTTGAACATTTGGAAATTCTTTTTAAACGTTTATCTGATTATGGAGTTGTTATTAATCCTTCAAAATGTGTTTTTGGCGTTTCATCTTTGGAATTTCTCGGACATAGCATTTCTGCAGATGGTATTTCCCCACTTCCACAGAAAGTTGCAGCTATTGCCGAATTTCCTGTACCTAATTCAATACGCAAACTCCGTGAATTTTTGGGTTTAATCAATTTTTATCGTCGTTTTATTCCTGACTGTGCTAGTATTATTCAACCGCTTACTGATCTTCTATCTCAGAAAAACAGTAAAGATACTTTTGAGCTTTCTGAAGAAGCCTTATCTGCGTTCTCTAATATCAAGTCTGCCTTAGCTAAAGCAACGTTGTTAGTCCACCCTTCACCCAACGCTCCATATTGTCTTATGGTCGATGCGTCCAATGTAGCCGTCGGTGGTGCTCTtcaacagaaaataaacaacatttgGCATCCGATTTCATTTTTCTCGAAGCGTTTACAGCCTGCTGAGACTAGATATAGTACATTTGGTCGTGAATTGCTAGCTGTTTATCTTAGTATTCGTCATTTTCGCCATTGTTTAGAAGGACGTGAATTTTTCATCCTTACCGATCACAAACCTTTGACTCACGCATTTTCCGCTTCTCCGGATCGATATTCACCTCGTGAAGTTCGCCATTTAGACTTTATTTCACAGTTTTCCACTGATATTAGACATATTCAAGGCAAAGAAAACTCAGTTGCAGATGCACTTTCTCGTGTAGATAGTATCAACGGTATTCAACCCTTACCAACATTAGACTTCGCAACGTTATCATCAGCTCAGAAAGATGACCCAGAATTATCTAAACTGTCTGAATCTTCATCGCTTAATCTTAAAGAATTACCTTTACCACTCACTTCTGGTACTATTATCTGTGATGTTTCTACTGATAATCCTCGTCCGTATGTTCCTGTATCCTTTCGTCGTCAAATCTTCGATCAACTTCATTCGCCATCTCACCCAGGAATTCGTGCTACTCAGAAATTAATTACTCAACGATTCGTATGGCCTAAGATTAATAAAGATGTTCGAAACTGGACTCAGTCATGCCTTCAATGTCAGAAATCAAAAGTTCAACGACATACTGTCGCTCCTCTTGGCACATTTCGCACTCCAGACGCTCGTTTCGACCATGTTCATCTTGACATAGTTGGCCCTCTACCACCTTCAAACGGACATCGTTATTTACTTACATGCATTGATCGTTTCACTCGTTGGCCAGAAGCCATTCCAATATCTGATATTACAGCTGAGACTGTTGCTCAAACCTTTGTTTCTCGCTGGATTTCTGTTTTTGGTGTTCCATCCACAATAACTACTGACCGCGGTGCACAATTTGAATCTTTGTTATTTCACAAACTAACCATATTGTTAGGCACTAAACGCATTCGCACAACATCATATCACCCTTGCGCAAACGGTATGGTTGAACGTTTACATCGCACCTTGAAAGCAGCACTTAAAGCCCAGCCTGATCCTTCTAAATGGACTGAAGCACTTCCTTTAATATTACTAAACATTCGCACTACAGTTAAAGAAGATTTACAATGTTCTCCAGCTCAACTTGTTTATGGTACTACCCTTCGATTACCTGCTGAATTCGTTGCCTCAGTTTCTGATTTTACTGATTTAGATCCCTCCGTTTATGCAGATCGTTTACGCCTTTTTATGCAACAACTTCGTCCTGTCTGTCCTCGTTCACAAGATCCTGCACATCACATTCCAAAAGATCTCAATCACTGCACTCATGTCTTTGTTCGTAATGACCGTGTTCGCAAACCTCTTCAGTCTCCGTATGATGGTccatttaaagttttaaaacgCACTTCAAAGCACTTCACCTTGGACATCAATGGTAAACGACAAACCATTAGTCTTGATCGTCTTAAAGTCGCCCATCTCGATTCAGATACCCAAGATACCCCTCAATCTCAGTCAAAACATACATCCTCTGCTGCTGCCGTACCAGCATTACCTCGTACTACTCGCTCTGGTCGGAAAGTTCATTTTCCAGATCGTTTTGGACAATGA

Transcript

evm.model.HiC_scaffold_248.6

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7LHG5	Transposon Ty3-I Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY3B-I PE=1 SV=2
Q99315	Transposon Ty3-G Gag-Pol polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=TY3B-G PE=1 SV=3
P0CT41	Transposon Tf2-12 polyprotein OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=Tf2-12 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000684 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan
PF00077 all species →	RVP	Retroviral aspartyl protease	Domain	Interproscan
PF17921 all species →	Integrase_H2C2	Integrase zinc binding domain	Domain	Interproscan
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF17919 all species →	RT_RNaseH_2	RNase H-like domain found in reverse transcriptase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR001969 all species →	Active_site	Aspartic peptidase, active site	Interproscan
IPR018061 all species →	Domain	Retropepsins	Interproscan
IPR041588 all species →	Domain	Integrase zinc-binding domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR021109 all species →	Homologous_superfamily	Aspartic peptidase domain superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR034132 all species →	Domain	Retropepsin Saci-like domain	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR041577 all species →	Domain	Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain	Interproscan
IPR001995 all species →	Domain	Peptidase A2A, retrovirus, catalytic	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR37984 all species →	PROTEIN CBG26694	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004190 all species →	Molecular Function	aspartic-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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 evm.model.HiC_scaffold_248.6.

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 →