Detailed information of PcrG022255.mRNA1 in Podabacia crustacea

Genomic Location: scaffold_45:2130172...2159739
NR annotation: no NCBI-NR hit recorded
Species Podabacia crustacea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003563 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00176
all species →
SNF2-rel_domSNF2-related domainDomainInterproscan
PF07533
all species →
BRKBRK domainDomainInterproscan
PF00385
all species →
ChromoChromo (CHRromatin Organisation MOdifier) domainDomainInterproscan
PF00271
all species →
Helicase_CHelicase conserved C-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR027417
all species →
Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR001650
all species →
DomainHelicase, C-terminal domain-likeInterproscan
IPR000953
all species →
DomainChromo/chromo shadow domainInterproscan
IPR016197
all species →
Homologous_superfamilyChromo-like domain superfamilyInterproscan
IPR000330
all species →
DomainSNF2, N-terminalInterproscan
IPR014001
all species →
DomainHelicase superfamily 1/2, ATP-binding domainInterproscan
IPR037259
all species →
Homologous_superfamilyBRK domain superfamilyInterproscan
IPR006576
all species →
DomainBRK domainInterproscan
IPR038718
all species →
Homologous_superfamilySNF2-like, N-terminal domain superfamilyInterproscan
IPR049730
all species →
DomainSNF2/RAD5-like, C-terminal helicase domainInterproscan
IPR023780
all species →
DomainChromo domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45623
all species →
CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000785
all species →
Cellular ComponentchromatinInterproscan
GO:0003677
all species →
Molecular FunctionDNA bindingInterproscan
GO:0003682
all species →
Molecular Functionchromatin bindingInterproscan
GO:0005634
all species →
Cellular ComponentnucleusInterproscan
GO:0006338
all species →
Biological Processchromatin remodelingInterproscan
GO:0010468
all species →
Biological Processregulation of gene expressionInterproscan
GO:0016887
all species →
Molecular FunctionATP hydrolysis activityInterproscan
GO:0042393
all species →
Molecular Functionhistone bindingInterproscan
GO:0140658
all species →
Molecular FunctionATP-dependent chromatin remodeler activityInterproscan
GO:0005524
all species →
Molecular FunctionATP bindingInterproscan
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan

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
K14437CHD7; chromodomain-helicase-DNA-binding protein 7EC:5.6.2.-
Chromosome and associated proteinsko03036deepkoala

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 Podabacia crustacea 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 Podabacia crustacea, 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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