Detailed information of ENSDLIP00000006650.1 in Diadumene lineata

Genomic Location: chr12:13605223...13613222
NR annotation: XP_020901624.1, DNA repair protein XRCC4 [Exaiptasia diaphana]
Species Diadumene lineata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006645 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF06632
all species →
XRCC4DNA double-strand break repair and V(D)J recombination protein XRCC4FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR038051
all species →
Homologous_superfamilyXRCC4-like, N-terminal domain superfamilyInterproscan
IPR010585
all species →
FamilyDNA repair protein XRCC4Interproscan
IPR014751
all species →
Homologous_superfamilyDNA repair protein XRCC4-like, C-terminalInterproscan
IPR009089
all species →
Homologous_superfamilyXRCC4, N-terminal domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR28559
all species →
DNA REPAIR PROTEIN XRCC4Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003677
all species →
Molecular FunctionDNA bindingInterproscan
GO:0005634
all species →
Cellular ComponentnucleusInterproscan
GO:0005958
all species →
Cellular ComponentDNA-dependent protein kinase-DNA ligase 4 complexInterproscan
GO:0006302
all species →
Biological Processdouble-strand break repairInterproscan
GO:0006303
all species →
Biological Processdouble-strand break repair via nonhomologous end joiningInterproscan
GO:0006310
all species →
Biological ProcessDNA recombinationInterproscan
GO:0010165
all species →
Biological Processresponse to X-rayInterproscan
GO:0032807
all species →
Cellular ComponentDNA ligase IV complexInterproscan
GO:0051103
all species →
Biological ProcessDNA ligation involved in DNA repairInterproscan
GO:0051351
all species →
Biological Processpositive regulation of ligase activityInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K10886XRCC4; DNA-repair protein XRCC4-DNA repair and recombination proteinsko03400deepkoala

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 Diadumene lineata 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 Diadumene lineata, 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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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