Gene detail

Detailed information of c1959.g001.t3 in Palythoa umbrosa

Genomic Location: c1959:218...16786
NR annotation: XP_028516059.1, uncharacterized protein LOC110243033 [Exaiptasia diaphana]
Species Palythoa umbrosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

c1959.g001.t3

ATGCAAAGAAATGCTATGGACTACAGATCAAGTGGCGTGAAGACAGTAAAACGATACGAACTGTTTGAACTAGCTTGTGTTTTGAGAGTTCGACCCCAACAACCGCACAGAAAATCGGCCAAAGGTAGTAACCATAGTAACTTATCACAGATCCAGTCTAGTGAGTGGCTTGAAATTGATGGTTATAATCTTCTCATACTTCTCTCCAGTAATGGCTCTCTTCTGTTGTGGAGTTGTGAAGAAGACAAAGCTGCTGTGGTAAAGCAgatcccatggtatcagTCTCCCTCAAAGGCAATCAAAGCATTCACCTTGGATCCAACAGGATCCTGGTTGGTTTGTGCATGTGCTGACGCAAACCTTTATATAGTGCCAATCGCTTCTGTTGTTAAGCAAACAACCAGACCATCTGCTCCTTCATATCCTTGGTCTGTAAATGACATCACATGTTTGAAGGTCAATGAAATAAGAGGCATTCCATCCAGTGTTGTATGGTGGCACACTGTTGATGATTTTGATATCTGTGTTGTCGGCACTGAGGCCGGAGAACTGTTGTTTATTGATCTCAAGACTGCTGAAGTAGTAATCGCAACAGATTTAAAAGAAAGTATTACAAGGCTGGAATTAATTAATGCCAAGAGCCAGGAGATTGCGTCACTTTTGGTCAGTAGCAGATCTGGTGAGACCTGGCAGGTTGTACTGGAGAGTAGAACTCTGCGTCGTCCAAGCCAAGAGCTTACCAGCCTACAGAGCCCTGGGGCAGCCTATGCACTCGGGTACGAGATGGTGGGAAAACTTGCGGTGCCACTTTTCAGCCTTTTAGGCAGTGAGACCAAAAACATGTTGGAGAGGTTAAAAGCAATGCCAGTAAAGACCAGTGGCAACGGGGGCGATGTAACATACTCTGTGCAACACGCACGAAACCAGGTCTTCATTGGGGCTCACAATCAAAGAACCgacgtgtttgagGTGTATGACGTTGACGCAGATCAATTGCCGATGTTTGTTTACCAGCTTCATCCGGGGACTTTAGAGATCGTTTTAACAGACAGATTGCTGTTTACTGTTATTCACTGCGAGGAAAATAAGAAAGCTGTTTATGTTCTTTCAAGTCAGCTGGCCGAGACATCAATTTCATCAACGAGATCATCACAGCGAGCACTAGAGTCTAGTGTTATACAGATTTTCTGTCTACCCAGCGATGAACAGGTTGTGGGCTTGTACAAGATCAGTAAGACTTTTGATTCAATTCTTGATCATCACATGAATGACAACATTGAGCCAGCATGCCTTAAGCCAGCAGAAAAAGCTGGTGGTGTGTGTGCAGTTGACGGCTGCGTCATTGTTACGTCGGCAGCAGTCTATGAGTGCAGGCCAAGACTCTCGCCAGAGAAGCTGTTTCTGGATCTTGCAGTTCATAACACAGATACAAACTCAGCGGACCTGCTGGCCATCACTGTAGGGCTGGACGTCAATGCCCTGTACCTGCTTGCAGCAGATCAGGCACTAGATGAAGGTCTATATGATCGAGCGATTAAGCTGTACCAGTTGTCCAAGTGTCCGTTTCCCATAAGAGTCGCGCAGTTTGCAAAACACGGAAGAATCTCAGATATCTTGGCTTATCTTCGCCAAGCGTTAAGTAAACACAGTGACGCTCACACAGCGGAGAGAAAGCAACTGTCAAATCTTGCGCTCTACTGTTTTGTGCAACAGATTTTGGAATCTGGGGGAGACATGGAAACTCAATCAACTTTGGCTGAAGCTTTCAGCCAATTCATAAACGACAATTTCGACTATGATGAGCGGTGTGCAATGGAGTTGTTGTCCGTTTATGGTCTCAAGGAGTACATGTTTGACGTGGCGAAGGCACGTGGATTGATGAGCGAAACCTTAGATCTACTGGCTAGTAAAGGACAATTCCATCTGTCCAGTAATATTCTTACTAAACTCGCTTCTCGGGGCTTCACCGATATCGTAAGCCGCAGCTGCAATGGTTCGTTTCTACAATGCATGGATCCAGCCGATGCGGTAAAATTTATTTTAGCTAAGCCAGAGACAATTCTGTCACATGTCACGCAACTCATGAACATGCTCATGGTTCTGGAAGAAGATATGCTGGTGCGTCTGTCACGCGTGACAGATCCTTCAAGACCTTCTTTTAGAACTCTAGCATCTCAAATCAAGCGCAATCCAAGAGGGAGATCTTTGTCTGTAGGCTCGGTTTCATCCTTGAGCTCGCTTGACAGTACAGCTAGCTTGAACCAGgaggaacatcgacgttgtccatttataatggacctggtacagctctttcttagtgcagtgctgTTTCAGGAGGAACATCGACGTGGTCCATCTATAATGGACCTGGTACAGCTCTTTTTTAGTGCAGTACTGGTACTAAATTACAGACGAGAACAAAAAATGGATTGTAACGCAAAGCTGGCCCTTACCAGGAAATTGTTGGATCCCCGAGGACGCAATGCGGACAACAGTGGGAGAAAGAAAGAAGGGGTTGCAGACACTGATTGGCAACAACAGACGCGACTTGCTTGTGGCCAGCAACACACAGCAGTGGTGAGCTCAACTGGGGATGTTTACACCTGGGGGAAATCACAGAAGGGAAGGTTAGGACACGGAGACCTCATAGAAGAAGAAGGAAAATCAGTGCCTTTCAGGGTTGAGATACTCCATATGCACAG

Transcript

c1959.g001.t3

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)	OG0002603 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00415 all species →	RCC1	Regulator of chromosome condensation (RCC1) repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000408 all species →	Repeat	Regulator of chromosome condensation, RCC1	Interproscan
IPR009091 all species →	Homologous_superfamily	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23323 all species →	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0006904 all species →	Biological Process	vesicle docking involved in exocytosis	Interproscan
GO:0007032 all species →	Biological Process	endosome organization	Interproscan
GO:0007033 all species →	Biological Process	vacuole organization	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0030897 all species →	Cellular Component	HOPS complex	Interproscan
GO:0048284 all species →	Biological Process	organelle fusion	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

No KEGG orthology assignment for c1959.g001.t3.

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 Palythoa umbrosa 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 Palythoa umbrosa, 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 →