Gene detail

Detailed information of RMX38676.1 in Pocillopora damicornis

Genomic Location: SczhEnG_3973:433574...437681
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_00005910

CCGGCCAAAACGGTTTTGTTCACATGGTCGTTTGACATAGTTAGAAATTTAGTTGAAGTCATCGATTCAGTTGTACTTTCTGTAGtctggttttaaaaaaatcatggcATTTGGTTGTTTACTCGTACTAGCCCTATTCTCATGCGTATTAGCAGAGGAGACAAAAATCTATTTTGTAGAGAAATTTGAAGACCAAAGTTATCAGGACAGATGGGTGGAATCCACTTTCAAAGGAAGTGACGCTGGAAAATTTACTTGGACTGCTGGAAAATTCTACGGTGATGCAGATTTAGACAAAGgtatTCAAACCAGCCAAGATGCTAAATTTTACGGTATTTCGGCCAAGTTTgaggaaagtttttcaaacgAAGACAAGACCTTTGTGATCCAGTTCCAAGTGAAACATGAACAGAACATCGACTGTGGTGGTGGTTACGTAAAGGTTTATGACAGCAAAGTGGACCAGAAGAACATTCATGGCGATACTCCATACCACATTATGTTCGGACCTGATATCTGTGGACCTGGCACCAAAAAAGTACACGTGATTTTTAACTACAAAGGGAAAAACTTGCTGACTAAGAAAGACATCAGATgcaagGATGATGAGTTCACCCATCTCTACACACTGATTGTGAAGTCTGATAACACCTATGAGGTTCGTATTGATGGAGAGAAGGTTGAAAGTGGCGAGCTTGAAGCTGACTGGGATTTTCTGCCACCAAAGAAGATAAAAGATCCTGAGGCCAAGAAACCAGAGGACTGGGATGATAAAAAGAAGATTGATGACCCAGAGGATAAGAAACCTGAGGATTGGGACAAGCCTCAGCACATCCCTGATCCTGATGCTAAGAAGCCTGATGACTGGGATGATGAGATTGATGGTGAATGGGAACCTCCAATGATCGACAACCCAGACTACAAGGGAGAATGGAAACCCAAACAGATTGACAATCCTAACTACAAGGGAGAGTGGATCCACCCAGAAATTGACAACCCTGAATACCAACCTGATGACAAACTTTACAAGTATGATGACATTGGTGCCATTGGATTTGATCTGTGGCAGGTTAAATCTGGAACCATTTTTGATAATATCCTTGTAACAGATTCTGTGGAGTATGCAGAACAATTTGCAAAGGAAACTTTTGAGAAAACCAAGgaaggtgaaaagaaaatgaaggatGAGCAGGATGAAAAGGAACgcaaagaaagagaggaagaagaaaagaagaggaaagaagaGGAGGACAAGAAGAAAGCagaggaagaagatgaagaggatgaggaagaggaagagGAAGAAGAAGGCAAAGAATCTGAGGAGGTAAAAGAAGATGAAACAGAGGAGGGTAAGGAAGAAACAGAAAGTGAAGAGAGTGCAAcagaagatgaagaaacaaaagccAAGGATGAACTTTAATTGAATCTGATGCATCTAGGCAtttttattgactgaaaaGATCTCCACAAAGCACACCTAATTAAATGGTGTGTGACTGAGATTTAGGTGGTGTATCAAATTGCTTCATGTGAAGAAgcttgcagaaaaaaaaaaagggcctCTTCATCATCTAGGTATacatttatcatttctttttagagGAAAATGTGGAAATACTGAATTGTTATCTGGTAATATTCTCTTGCTCTTTGCTGGGTTAAATTTGTTATAATCTTTTTCTAGCATGGAAAGGCCTATCTCCTGTGGTTACTCTTGCTGTAGTTACCAGaactaatttaatttcttgtttattaaaaaaaaaatgatgagaaaCAACTGTGTCACAGTTTGCTTCCTACCTCATTGTGTTGTGGCATTTGTGCTTCCCTGCATTGAAAGCCCCGATTAAAAAGGGAACTGAGAATTTGTGTAATGACATGAAAACCATCTGGATTGTATAATGAATGGAATTAACCATATGGAGtacttttatttctcaaaatggTATCATGCAAAATAGGGGAAACAGGTTGAACAATAGactaattgttaatttgtaTTGGAAGAAGAAACTAAATTAATGCTCTAACTATCATAGttgatcaacatgtaacttctcatagtattcatacattatccagcaaaaaggtaatgagaatactcgGTCTCATCAGGTAGatgttgtcatcttgatcGAAAACCAGACTTGGACAAataaatatgtagcagctagaggggaggattaacagtcagatcttgggagttcaag

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P11012	Calreticulin OS=Onchocerca volvulus OX=6282 GN=crt-1 PE=2 SV=2
P14211	Calreticulin OS=Mus musculus OX=10090 GN=Calr PE=1 SV=1
Q4VIT5	Calreticulin OS=Chlorocebus aethiops OX=9534 GN=CALR PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007668 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00262 all species →	Calreticulin	Calreticulin family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009033 all species →	Homologous_superfamily	Calreticulin/calnexin, P domain superfamily	Interproscan
IPR001580 all species →	Family	Calreticulin/calnexin	Interproscan
IPR018124 all species →	Conserved_site	Calreticulin/calnexin, conserved site	Interproscan
IPR009169 all species →	Family	Calreticulin	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11073 all species →	CALRETICULIN AND CALNEXIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0006457 all species →	Biological Process	protein folding	Interproscan
GO:0051082 all species →	Molecular Function	unfolded protein binding	Interproscan
GO:0005789 all species →	Cellular Component	endoplasmic reticulum membrane	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	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
K08057	CALR; calreticulin	-	Lectins	ko04091	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 →