Gene detail

Detailed information of RMX57509.1 in Pocillopora damicornis

Genomic Location: SczhEnG_647:175877...180218
NR annotation: no NCBI-NR hit recorded
Species Pocillopora damicornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-pdam_00005769

tttagaatgtaTCGTCTATCAAGTGTGATCCGTCCGGCCAGACAGCTGTTCACTCCAAAAATCTTGGCCCCTCGGCTTGCTGTTGGGTTCAGCACCTCACAGCAACAACAGTCCGCCAAGGAGCTCAAGTTTGGGGCTGATGCAAGATCCAATATGCTTAAAGGAGTTGACACCTTAGCTGATGCAGTTGCAGTCACTTTGGGTCCAAAGggaaaaaatgttataattGAACAAAGCTTTGGAGGCCCAAAGATCACTAAGGATGGTGTAACAGTTGCCAAAGCCATTGAACTGAAAGACAGGTATCAGAACATTGGTGCTCGTCTTGTGCAAGATGTTGCCAACAACACTAATGAAGAGGCTGGAGATGGAACAACAACTGCAACTGTCCTGGCCAGGTCCATTGCCAAAGAAGGCTTTGAGATTGTTTCCAAGGGAGCAAATCCTCAGGAGGTTAGGAAAGGTGTTATGCTGTCAGTTGAAGCTATTGTTGAAAACCTAAAGAAAATGTCCAAACCAGTTACTACTCCAGAAGAAATTGCTCAGGTTGCAACAATTTCTGCTAATGGCGACAAAGGCATCGGAGAACTGATCTCCTCAGCTATGAAAAAAGTTGGCAAGAATGGAGTGATCACTGTGAAGgaTGGCAAGACCCTGTATGATGAGTTGGAATTGATTGAAGGAATGAAGTTTGACCGTGGATTCATTTCTCCCTATTTTATCAACACTACAAAAGGACAAAAGGTTGAGTTCCAGGATTGTTTGGTTCTCCTGTGCCAGAAGAAGATCTCTTCCATTCAACAGATTGTTCCTGCGCTTGAGCTGGCTAATGCACACAGGAAACCTCTTGTTATTGTAGCAGAGGATGTTGATGGTGAAGCTCTGACTACACTTGTCCTCAACAGGCTCAAAGTTGGTCTCCAAGTGGCTGCAGTGAAGGCACCAGGTTTTGGTGACAATCGCAAGAACACGCTGCAAGACATGGCCACTGCCATGGGTGGTATGGTATTTGGAGATGATGCTctggaaacaaaacttgaagATGTCCAAATTCAAGATCTTGGTGAGGTTGGAGAAGTGTCAATCACTAAGGATGACACGCTGTTCTTAAAAGGAAAGGGTAGCACAGAGGAAATTGAGAAGAGGTGTGCTCAACTCAGAGAGGAGCTTGAAAATACAACTTCAGAAtatgagaaagagaaaataaatgaacgtCTGGCCAAGCTCTCTGATGGTGTTGCTATCTTGAAGATTGGTGGTTCCAGTGAAGTAGAAGTGAATGAAAAGAAGGACCGGGTAACAGATGCTTTGAATGCCACCAGAGCAGCTGTGGAAGAAGGTCTTGTGCCTGGGGGTGGTGTTGCCTTGTTGAGATGTATCCCCAGCCTTGATGACATCAAGACAGAAGGTGAAGACCAAGCCAAGGGAGTAGACCTTGTCAGACGGGCTCTGCGTAAGCCATGTCAGACTATTGCAGAGAATGCTGGTGTAGAGGCAGCACTTGTGGTGGAAAAGGTGGCCTCTATGGAAGGTAACCAAGGTTACGATGCCCTTAACAACACCTACGTAGACATGATCCAAACAGGAATCATCGACCCCACAAAAGTTGTCAGAACAGCTGTGACAGATGCTGCAGGTGTTGCATCCCTCTTAACCACAGCAGAAACAGTCATTGTTGATCAGCCCAAGGATGACAAGGCAGACATGGCTGGCATGGGTGGAATGGGAGGAATGGGCGGAATGGGTGGAATGGGAGGAATGGGTGGAATGGGtggattttaaatgaatggaTGAGATATTATTCAATGTGCTTTGGTTCCCTAATTTCACAACTTGCATATCTGGAAACATTTATGTTTAACAGTAGCTCATAATGCTCTGGATGTTCAAGACTGTGTGATCTTTGAACTGTGGTCTCCCTATACTGTTTATGGATCAAGTGCATTTTCTGGAAAATCAGACAGAATGCTGGCTTGCAAAGACAGCTGATTTGATGATCATAGCTAAAACACCagctaaaacagaaaaaaaaaattggctggttcaaattttgcagGCTAGCATAGCATGCAcattgtaaaaattacaataagaCTGAATTAAAGTTGGGTTTATGCATAGGTCTCTGTGCAGAGAATTCAGTTTTAGCTGTGTAGATCCATGCAATAGCTTGGGTAAATTAGTTCATGCATTATGAATTCTTTTCACTTGCATTGCTAAGTAGATTGCATTTCTGGTGCTCCATCTCAATAAAATCGTTTTT

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006322 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00118 all species →	Cpn60_TCP1	TCP-1/cpn60 chaperonin family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027410 all species →	Homologous_superfamily	TCP-1-like chaperonin intermediate domain superfamily	Interproscan
IPR001844 all species →	Family	Chaperonin Cpn60/GroEL	Interproscan
IPR002423 all species →	Family	Chaperonin Cpn60/GroEL/TCP-1 family	Interproscan
IPR027409 all species →	Homologous_superfamily	GroEL-like apical domain superfamily	Interproscan
IPR018370 all species →	Conserved_site	Chaperonin Cpn60, conserved site	Interproscan
IPR027413 all species →	Homologous_superfamily	GroEL-like equatorial domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45633 all species →	60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0042026 all species →	Biological Process	protein refolding	Interproscan
GO:0140662 all species →	Molecular Function	ATP-dependent protein folding chaperone	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006457 all species →	Biological Process	protein folding	Interproscan
GO:0005743 all species →	Cellular Component	mitochondrial inner membrane	Interproscan
GO:0005759 all species →	Cellular Component	mitochondrial matrix	Interproscan
GO:0008637 all species →	Biological Process	apoptotic mitochondrial changes	Interproscan
GO:0034514 all species →	Biological Process	mitochondrial unfolded protein response	Interproscan
GO:0045041 all species →	Biological Process	protein import into mitochondrial intermembrane space	Interproscan
GO:0051087 all species →	Molecular Function	protein-folding chaperone 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
K04077	groEL, HSPD1; chaperonin GroEL	EC:5.6.1.7	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 Pocillopora damicornis 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 Pocillopora damicornis, 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 →