Gene detail

Detailed information of ENSPYFP00000033737.1 in Pteroeides griseum

Genomic Location: chr8:18931173...18941672
NR annotation: no NCBI-NR hit recorded
Species Pteroeides griseum · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSPYFT00000035765

gtaaaaacaaagaaaaagttGGATGTCGATAAAAAATCTATcaagaaagaaaaaacaaaaaacaaagtgaAAAAAGAAGTAAAAAAGGAAGGAAAAAAAGAAGCTGTGAAAAAAGAGGTTGCTGGGTTTTATGCCAAGATGTTGGATCATGAATACACATCAAAGAAaatttttaatgacaactttttTGAAGATTGGAGGAAAGAAATGAACGATGAGGAAAGAAAGTTGATTAAAGATATATCAAAATGTGGTTTTCAAGAATTACACGCTTATTATGTCCAGGCAAAAAAATGAAGAGAGAAAAAACATGACGAAAGAGGACAAACAGAAACTCAAAGAAAAGAACGAACAGATCCTCCAGGAATATGGTTATTGTATGATGGATGGACATAAAGAAAGAGTTGGTAATTTTAAAATTGAACCTCCTGGTTTATTTCGTGGTCGTGGAGATCATCCGAAACAAGGAAAGTTCAAAAAAAGAGTGAATGCAAAAgatgttattattaatattggaaaagATGCTAAGGTGCCAGGTCCACCAGAAGGTCAAAAATGGAAAGCGGTAACATATGATAATAAGgTCACATGGTTGGCATGTTGGATTGAAAATATCCAGGGAGGTTATAAATACGTTATGCTTAATCCTACATCACGTATTAAGGGTGAAAAAGATTGGCAAAAATACGAAACGGCTAGAAAACTGAAGaCTAAAGTTGGTAAAATCCGAAGTGATTACTCAAACGATTGGAGGTCTAAGGAAATGCGTCTCAGACAAagAGGAGTGGCGTTGTACTTTATTGACAAGCTTGCTCTTCGTGCTGGTCACGAAAAAGATGAAGACACTGCAGATACAGTTGGTTGTTGTTCACTACGAGTGGAGCACATAAaacttcaccgtgaaaaagataACAAGGAGTATGTTGTAGAATTTGATTTTCTTGGTAAAGATTCTATCCACTACCACAATTTAGTTGAAGTAGAAAAAAGGgtTTTTAAAAATCTAGAATTATTCAAGCAAGGAAAAAGTGATGGAGATGATCTGTTTGATCGTCTTTCGACAACGTCGTTAAACAAATATTTATCGGAGTTAATGGAAGGTCTCAGTGCTAAGGTCTTTCGTACATATAACGCTTCAATGACATTACAAGAACAGTTAAATAAACTGGAAGTTGAAGACAACGTAGCATCTAAAGTATTAGGATATAATCGAGCTAATAGAGCGGTGGCTATACTATGTAACCATCAGCGTACAGCTCCTAAAACGTTTGAACAATCAATGTCAAATCTTCAACAAAAGATTGAAGACAAACGAAAATTGATCAAAGAAGCTAAGAAAGAGACGAAAGACCTGAAAGCAGAAGCGAAAGCTAGTAAAACACCTGCAGCGGAGAAGAAATatgaaaaaaagaaaacaacttTAGCTAGATTACAAGAACAGTTATTTAAACTTGAGGTCACGCAAACCGACAAGGAAGAAAACAAGGAAATAGCGTTAGGGACatcaaaattaaattatttagatCCAAGGATATCAATAGCTTGGTGTCGAAAGAATGATGTCCCGATAGAAAAAATTTACAACAAAACCCAACGGCAGAAGTTTGCTTGGGCTATAGACATGACTGAAGAagattttgtattttaaatcaTTTGCATTTCTTTTTACAATTTTAAAGTACTTTTTATTTCTCAATCTCTCGGTGATCGAAGAGCGGAGAGTTTTTATCGACACAAAGTTTTACACACACCGACGTTTTCCTAACAGTAAACCTCTATGCTGGTAAAATGTTACGAGATGGGACAAGAGAGAAGCTGCAGATAACTGAAGAATTACAATGTTGCTGCTTTTGTTTTGCATATTATGTCGTCGTGCAGTTATAATGGTAAAATGTTACGAGATGGGACAAGAGAGAAGCTGCAGATAACTGAAGAATTACAATGTTGCTGCTTTTGTTTTGCATATTATGTCGTCGTGTGCAGTTACCATATTTGACGACGAAAGTTCTTGGAAACGTACACGAATTTCCCAGAAATGGCAAATTGTATAACTTGCAAATTCTGCTGAAATCGATTTAGAATTGTTAGTTATTTATGTCGTTATATCGCGGCCTAGTATGAAATGTAATATACGCCGCAAAGAGCAACTAAACAAtcttacaaaatatttaataaacagAATCTAATCAAGTGCTTTGATTTTATGTATATCTTTTGCGGCTCtatgtgacgtcataatgacGTATTTGTTGAGACAAGTTCGATATTGTATTTTTACAATTGCTCACGAGATGTCTGTCATAAAATGTTGTAACAATGTGTATCGTAAAATGGAATTTGGTCTCTGACTTTAGCGCGTTTA

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004961 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02919 all species →	Topoisom_I_N	Eukaryotic DNA topoisomerase I, DNA binding fragment	Family	Interproscan
PF01028 all species →	Topoisom_I	Eukaryotic DNA topoisomerase I, catalytic core	Domain	Interproscan
PF14370 all species →	Topo_C_assoc	C-terminal topoisomerase domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR014727 all species →	Homologous_superfamily	DNA topoisomerase I, catalytic core, alpha/beta subdomain	Interproscan
IPR011010 all species →	Homologous_superfamily	DNA breaking-rejoining enzyme, catalytic core	Interproscan
IPR008336 all species →	Domain	DNA topoisomerase I, DNA binding, eukaryotic-type	Interproscan
IPR051062 all species →	Family	DNA topoisomerase IB	Interproscan
IPR018521 all species →	Active_site	DNA topoisomerase I, active site	Interproscan
IPR013499 all species →	Domain	DNA topoisomerase I, eukaryotic-type	Interproscan
IPR013500 all species →	Domain	DNA topoisomerase I, catalytic core, eukaryotic-type	Interproscan
IPR001631 all species →	Family	DNA topoisomerase I	Interproscan
IPR013030 all species →	Homologous_superfamily	DNA topoisomerase I, DNA binding, N-terminal domain 2	Interproscan
IPR025834 all species →	Domain	Topoisomerase I C-terminal domain	Interproscan
IPR036202 all species →	Homologous_superfamily	DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily	Interproscan
IPR014711 all species →	Homologous_superfamily	DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10290 all species →	DNA TOPOISOMERASE I	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003917 all species →	Molecular Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	Interproscan
GO:0005694 all species →	Cellular Component	chromosome	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0006260 all species →	Biological Process	DNA replication	Interproscan
GO:0007059 all species →	Biological Process	chromosome segregation	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
K03163	TOP1; DNA topoisomerase I	EC:5.6.2.1	DNA replication proteins	ko03032	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 Pteroeides griseum 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 Pteroeides griseum, 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 →