Gene detail

Detailed information of evm.model.HiC_scaffold_2.252 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_2:3291637...3314502
NR annotation: XP_028399776.1, xanthine dehydrogenase/oxidase-like isoform X2 [Dendronephthya gigantea]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_2.252

ATGCCGGCATCAGTACACGATTTGATTGAAGGTCCAGTCAATAAAGACAGCCATAAAACAGAGAAGGTTAAACTGACTGTCGCATATGACAATGTCAGGACAATCCATCTCACTGTCAATGGAATCAGCTATACGGTATCCAATGCTGATCCTAAAATGCTCCTCAATGATTGGCTGAGAAATCATTTACACTTAAAAGGGACGAAAGTACTTTGCGCAGAAGGGGGGTGTGGTTGCTGTGTTGTAGCGATTTCAAAAGACGACCCCTTGACTCAGCCGGAATCAATTACGGCTGTTAATTCCTGCTTGTGCCCTCTTCTCTCTTTGGATGGTTACCATGTTATAACAGTAGAAGGTCTTGGCGGACAAAAAGATGGTTTTCACGTTATTCAGAAACGGTTTGCTGAAAAGTTTGCAAGTCAATGTGGATTTTGCACTCCTGGGTTTGTTATGAATGGCTTTAGCTTGCTGGCCTCTACCAAAAATGGGAAAACGACCAAAGAAATGGAAGATAGTTTCGATGGAAATATTTGTCGTTGCACAGGTTATCGTCCAATATTGGATACTGTAAAATCACTTGCGAAAGGCAGTGATATTGCTGATATTGAGGAGTTGAGGAGCTGCAAAGgttgcaagaaagactgcaaAAAAGCAAGGTCTATTGACTACCAACACGAACCCAATTCAGAATCGCAATGGTATTCACCTGGTTCTCTATCAGAGATATACCACATCTTTCAAAGGAACAGGGGTAGGAGATTGAAAATCATATCTGGAAATACTGGAGTTGGAGTCTTCAAGAACGAAGGATATTTTGATGGATTCATCAATGTTAAAGACATGAAGGAGCTTGCAAGAGTTGAGatAAAAAATGAAACACTGGAAATTGGTGCAGCTGTAACACTGACCCAGTTGGTTAATTTTCTCGAAATGAACACTGAAAAGTCAAAGTCGTTTGCTGTCTTAGCTTCACATATCAAAAAGgttGCTAATGTCCCCGTGAGAAACGTTGCAACATGGTCAGGCAATTTGATGCTAATCCATGCACATAAGCATTTCCCATCCGATATATACCTTATGTTTGATGCTGCTGGAGCAAAGGTTTCTTTAGCTGATTTAAACGGCAATACCATGTACTGCACACTTGGGGAATTCTTGCAAACACCGATGGTTTCGAAGATTATCGTGCATTTGTCTCTTCCCTTAACTCAATCTGATGAGGTTTTCCAAACGTACAAAATAATGCCAAGAAAACAGGTCAGAGCTGTCAGAGTAGAGGATTATTTGTATAAGAAGTCCTTGGAAGCCAAACATGTTTTTAAAGATGCCTTGAAATTACTAGAAGATTACTTGCAGCCAAATCCAGAGAACAAGCTTATTGATTTCGCCTATTGCAAGAATGTTGCATCCAATTTGTTTTATAAGTTTGTTACCCTTCTTCGTGGAGAGAGAATAAACAAAAGGCTACTTAGCATTACTAAACCACTTGAACGTCCAGTATCTTCTGGACAGCAGTTTTTCCATGTGGAGGAAAAATCTGCTCCGCTCAATCAACCACGAGAGAGAATCGAAGGAAATTGCAGGCTTCTGGAGAAGTTCTATTTGTTGATGACTTGCCAAAACATCCAGATGAAGCATATGCTGCCTTCGTATTATCTGAGTTGGTTTGATTTTCACTTTTTACTTAAACCTCCTTTTGACCTGTTTTTACCGTCTGCAGGGAAATGCAACACTGAAAGGAATCAATTCGAGGAGGCTGAGAAATGTCCTGGCTTCATCGCCGTGTTGACTGACAAAGACATCCCAGGGATCAACAATTTTTATGGCAAGGGACCGAATCATGAAGAGATATTTGCAAGTAAAGACGTCGAGTATGCAGGACAGCCAGTCGCACTGGTCGTAGCGAGTTCACAAGCAGCAGCCAACGAAATCGCTAAACTCGTGACGATCGAATACTCTGATGTTCGTAAGCCAGTCACTACGATTGAAGAGGCCATTACAATGAAGCAATTCCATACCGCAAATATTCCTGACAATATAATTGGAAATACAGAAGATGCCTTTCCGAAATGTGATCATGTGATAACAGGGGAAATCAAATCTGGTGCGCAGCAGCATTTCTACATCGAGCCTCTGACATGCTATGTTGTGCGGGAAGAACACGATTACAAAGTATTTTGTTCAACACAAAGTACAATGGATGTGCAAGCTGCGATTTCTAACGCTCTTGCGGTAAACATTGCAAGTGTTGATGTCAAAGTGACTCGCATTGGTGGAGGATTCGGAGGAAAATACCAATATCCACCACTTATTGCTGCTGCTACTGCCGTCGCTGCTAAAGCCCTGGATAGGCCTATTCGTATGGCGATGACTCTAACTGACAACTTGAAAGTGAGCGGAATGAGGCCGTCTTTTCTAACCAAGTATAAGGTTGGATTTTCTAAAGAAGGATACCTCGAAGCTTGCGATATTAGCATATTCGTTGATGCTGGAAAGTCTCTTCATTGTGCAGATGGTGAAAGAGCATCTGTGTGGATGGATAATGCCTATTTCTGCCCAAATTGGAAGATTTCCGTCACCAactgcaaaacaaacaaaccgTTCAACACGTTTTTCCGAGGACCAGGAAACATTCAAGGTGTTTTCGTTATGGAAACTATTCTTGACCATGTCGCAACTTTCCTGAAGAAAGAATCTGCTGAGGACATAATGGAGATCAATCTCTATAGAAATGGTCAGATGTCATTGCGAGGAATAAAAGTCTCTGATTGTCTATTGCATAGCATATGGGCAGATATACATTTGAAATCTGACTACAAGATGAGACAAATTGCAGTTGCAAAGTTTAATAAGGAAAATAGATGGAAGAAAAGAGGATTGTCAATCATGCCAATGAAATATGACATTAACTATTTTATCCTAAGCTTCCCAGCCCTCGTTTCAATTTACTATGGAGATGGAACGGTTGCAGTTTCTCATGGTGGCATTGAAATGGGTCAAGGAATAAATACAAGGGTTCGTACTGTTGCTGCTGCCAAGTTAGGCATACCTGTTGAAGATGTATCAGTGAAGCCACACTCGACAATAACCGCTGCCAACTCATTTGAGACGGGTGCTAGCGTGACGTCAGAAATGAATTGCTTgGCAGTGTACAAATGCTGTGAAATTCTATGTCAACGAATCGCCCCAGTCAAAGAGAAGTTTCCTGGGTTGAATTGGAAAGATCTGATAAGAAAATGTGCTGAATTGAAAGTTGACCTGTCTGCTCAGCTACAgTATCAAGATCCTAAGAAAGTCGAATTTGCCTACTCTGTTTACGGTGCTGCCTGCTCTGAAGCAGAAATCGATGTTCTAACTGGAGAAACTCACATTTTACGATCAGATATCATTTATGACTGTGGAGAAAGCATAAACCCAAGACTAGACATTGGGCAAATAGAAGGAGCATTTGTTCAAGGAATGGGATATTGGTTGACTGAAAAAGTTGTATTTGATCAggaaaatggacaaaaattaaCAACCAGCACTTGGGACTATAAACCACCGATGTCAAAAGATATTCCCATTGATATGAGAGTGTATTTGTCACATGATGCAACAAATCCTGTTGGTTTAATTCGTTCTAAAGCTGTTGGTGAGCCAGCTATCTGCATGTCTGCATCTTGCCTCTTTGCTgccaaaaatgcaataaaagctGCCAGAACAGAGCTTGGAAAACCTCTGGAATATTTTACTTTAGatgGCCCTGCGACCATGGATAAGATACAGAAACTTTGTCAAATTGATCACAAGGATCTCCTATTCGACTAA

Transcript

evm.model.HiC_scaffold_2.252

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q54FB7	Xanthine dehydrogenase OS=Dictyostelium discoideum OX=44689 GN=xdh PE=3 SV=1
Q6AUV1	Xanthine dehydrogenase OS=Oryza sativa subsp. japonica OX=39947 GN=XDH PE=2 SV=1
P80457	Xanthine dehydrogenase/oxidase OS=Bos taurus OX=9913 GN=XDH PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000566 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF20256 all species →	MoCoBD_2	Molybdopterin cofactor-binding domain	Domain	Interproscan
PF02738 all species →	MoCoBD_1	Molybdopterin cofactor-binding domain	Domain	Interproscan
PF01315 all species →	Ald_Xan_dh_C	Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain	Domain	Interproscan
PF00111 all species →	Fer2	2Fe-2S iron-sulfur cluster binding domain	Domain	Interproscan
PF01799 all species →	Fer2_2	[2Fe-2S] binding domain	Domain	Interproscan
PF00941 all species →	FAD_binding_5	FAD binding domain in molybdopterin dehydrogenase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR046867 all species →	Domain	Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain	Interproscan
IPR037165 all species →	Homologous_superfamily	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily	Interproscan
IPR036856 all species →	Homologous_superfamily	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily	Interproscan
IPR016169 all species →	Homologous_superfamily	FAD-binding, type PCMH, subdomain 2	Interproscan
IPR001041 all species →	Domain	2Fe-2S ferredoxin-type iron-sulfur binding domain	Interproscan
IPR008274 all species →	Domain	Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain	Interproscan
IPR036884 all species →	Homologous_superfamily	[2Fe-2S]-binding domain superfamily	Interproscan
IPR000674 all species →	Domain	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead	Interproscan
IPR012675 all species →	Homologous_superfamily	Beta-grasp domain superfamily	Interproscan
IPR036010 all species →	Homologous_superfamily	2Fe-2S ferredoxin-like superfamily	Interproscan
IPR002888 all species →	Domain	[2Fe-2S]-binding	Interproscan
IPR036318 all species →	Homologous_superfamily	FAD-binding, type PCMH-like superfamily	Interproscan
IPR002346 all species →	Domain	Molybdopterin dehydrogenase, FAD-binding	Interproscan
IPR016208 all species →	Family	Aldehyde oxidase/xanthine dehydrogenase-like	Interproscan
IPR016166 all species →	Domain	FAD-binding domain, PCMH-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11908 all species →	XANTHINE DEHYDROGENASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0051536 all species →	Molecular Function	iron-sulfur cluster binding	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0005506 all species →	Molecular Function	iron ion binding	Interproscan
GO:0071949 all species →	Molecular Function	FAD 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
K00106	XDH; xanthine dehydrogenase/oxidase	EC:1.17.1.4 EC:1.17.3.2	Exosome	ko04147	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 →