Gene detail

Detailed information of RMX55311.1 in Pocillopora damicornis

Genomic Location: SczhEnG_1087:43709...52595
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_00022874

GCTGTGGCCATTGTCTGACCACAGttgaatttcttatttcattccATCGAGGCCGCCAATCTTttggccagaaaaaaaattataaaaatggGTGTAAAATTTCTCGAAGTACTACGACCATTTATTTCCGTTCTGCCTGAGGTCTCAAAGCCCGAAAGAAAGATCCAGTTTAGAGAGAAAGTACTATGGACGGCGATTACGCTGTTTATCTTTCTTGTCTGCTGCCAGATTCCTTTGTTTGGCATTATGTCGTCGGATTCAGCTGATCCCTTCTACTGGATGCGAGTGATTTTAGCTTCGAACAGAGgtACCCTCATGGAACTTGGTATATCCCCAATTGTCACTTCAGGACTTATTATGCAGCTTTTGGCAGGTTCTAAAATTATTGAAGTTGGTGACAGTCCAAAAGACAGAGCTCTCTTCAATGGATCTCAAAAGTtGTTTGGTATGATCATTACCATTGGCCAAGCTGTTGTGTATGTTATGACTGGAATGTATGGTGATCCTTCTGATCTTGGCCCTGGTATCTGCCTTCTGATTATCATCCAGCTGTTCTGTGCTGGTCTTATTGTTCTCTTGCTGGATGAACTTCTTCAGAAAGGATATGGCCTTGGATCAGGAATCTCACTGTTCATTGCCACAAACATCTGTGAGACTATTGTTTGGAAAGCATTCAGTCCAGCCACTATTAACACTGGCAGGGGTACTGAGTTTGAGGGTGCTATCATTGCCTTGTTCCATCTGTTGGCCACCAGAACAGACAAAGTGCGTGGGCTCCGTGAAGCTGTCCATCGTCAGAACCTACCAAACATCACTAACCTGATTGCcacaatttttgtctttggtATAGTTATTTACTTCCAGGGCTTCCGTGTAGATCTTCCCATCAAGTCTGCTCGCTACAGAGGCCAATACAGCTCTTACCCAATCAAACTGTTTTACACTTCAAATATTCCCATCATTTTGCAGAGTGCCCTCGTGTCCAATATTTATGTCATTTCCCAAATGTTGTCCACTAAGTTTGCTGGAAATTTCTTCGTCAGTCTTCTTGGAACATGGGAGGAAGCTGGTGGTGGACCTGCGCGATCATACCCCACTGGTGGCCTGTGCTATTACATGTCACCTCCAGAGACAGTGAGTCACATCATAGAAGATCCCATTCATGCCGTCTTGTACATCGTGTTCATGTTGGGCTCTTGTGCTTTCTTCTCCAAGACATGGATTGATGTGTCTGGCTCCTCAGCTAAAGATGTTGCCAAACAGCTGAAGGAACAGCAAATGGTGATGCGTGGACACCGCGATAAATCCATGGTCCATGAACTCAACAGGTATATCCCTACAGCTGCAGCTTTTGGTGGACTTTGTATTGGTGCCCTTTCAGTCTTGGCTGATTTCATGGGTGCCATTGGCTCAGGAACAGGTATTCTGTTGGCTGTCACCATCATTTACCAATACTTTGAAATCTTCGTTAAAGAGCAAAGCGAAATGGGAGGCATGGGAACTCTCCTGTTTTAAACAAGCCATTCTGCACTGTATCAACCATCCCATAAAATTACCACTGTACTTAATATCCAGCCTAAGAATGgaagtttttctctctcttgaattctgtttattttgtgattgaaaaatgaaatttcaccTTGTATTAGCTTATTTGTACTCTTGTAAGTTAAAGAAAACTGCTCAAAAGATTTGCTATTTTAGTGagacattaaaattttatcagcaGAGATAATTTTGCCATCCCATTAACCAGGCTCAactgtacaaaaaaattggtggCTGACCTCGTGGCTATACATGGACttgtaaagtttttcttccttttctattttattaaattttatggcCAACTTCCTTCTCAAAGCAGGGTTGTAGAGTGTGTTTCCTCTTCACtgtctttccttgtttttatGTGTTTGAGGTGAATGGCCAGGCTCCCTTGAAAGCGGTGCAATGCCTGGTGGCATGAGAGAGGCAGCAATAAGAAAGACTGTGAAAGAAAGGCTAGGTGAAGAGTACTGGAAGGTACTCTGCATTACGAATATTCACTTGGTTAGAAGATGGTATTCTCATACAGTATTTCACTTTGCAAATTGTTGACTAGGGTCGTTGCAGTAGATacttaaatttcaatattATCTGCCTTTATTGTATTTCGATACTGGTTAATGGAAGGTTCGTTTTGCAAAGATTAAAAGTGATACTTGCATCTCACccacataaataaataaacaaataaagtgCCTTGTGTGAA

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)	OG0007598 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10559 all species →	Plug_translocon	Plug domain of Sec61p	Domain	Interproscan
PF00344 all species →	SecY	SecY	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002208 all species →	Family	SecY/SEC61-alpha family	Interproscan
IPR030659 all species →	Conserved_site	SecY conserved site	Interproscan
IPR019561 all species →	Domain	Translocon Sec61/SecY, plug domain	Interproscan
IPR023201 all species →	Homologous_superfamily	SecY domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10906 all species →	SECY/SEC61-ALPHA FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005048 all species →	Molecular Function	signal sequence binding	Interproscan
GO:0005784 all species →	Cellular Component	Sec61 translocon complex	Interproscan
GO:0006616 all species →	Biological Process	SRP-dependent cotranslational protein targeting to membrane, translocation	Interproscan
GO:0008320 all species →	Molecular Function	protein transmembrane transporter activity	Interproscan
GO:0015031 all species →	Biological Process	protein transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0031204 all species →	Biological Process	post-translational protein targeting to membrane, translocation	Interproscan
GO:0043022 all species →	Molecular Function	ribosome 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
K10956	SEC61A; protein transport protein SEC61 subunit alpha	-	Secretion system	ko02044	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 →