Gene detail

Detailed information of ENSHHBP00000020783.1 in Porites divaricata

Genomic Location: chr5:4477261...4487523
NR annotation: no NCBI-NR hit recorded
Species Porites divaricata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSHHBT00000024277

GGTGTGTGAGCTATAAGTTTCCGCAAGCGTCGAGAAAAGCCCTCAGCTGTGAGGGTGAAGTTTCCAACCGGACCAAAACGAGAATTTGTCCTTCGTGGATGAATTTGGAGCCAGGTTTTAAGgaTACCCATGGTATTTAGCATTATTTTAAGTTAAGCTGCAATCTGCTATAGCTGAAATCAATCATGCCGATACAAACCCCTCAGTGGACAGAATTTTTACAGTGTCCAATATGTACCAACGACTTCGACGAACACACCAGACAGCCAATCAGCCTTGGATGTGGCCACACAATGTGCATTTCTTGCTTATCAAAGCTCCCGAGAACACAGTGTCCATTTGACCAGGCTATTGTTGACACAGACATTTCCAAGCTTCCTTACAACTATGCTCTGCTTCAGTTAGTTGGAGTAGAAGTGCCAGATGATTCACTTCCAGCCATAGAAAGTGTACGGGACAATGCAGATCAATATCGAGCGGCCAAACGTGCTATTGAAGAACTTGCACTGTTTTTACAACCTGTGTCCAGTGCTCCAAATGGAATAGTTAATGGTAATGGCAATGGAAGTGCTTGTATTGGTTCTCTTAATGGAAGTGGAAACAGTATACTTACAAGACCAATGCAGCGTAAGCTGGTTACTTTAATAAACTGTCAGATTGCTGAAGTTGACGGACGAACGAGGGCTATGCGTGCAGCAAGAAGCCTTGGAGAAAGAACAGTTACAGAGCTTATTTTATTACACCAAAATCAGCAACAATTATCAGCAAATTTATGGGCTGCAGTGAGGAACCGTGGTTGTCAGTTTTTAGGACCAGCAATGCAAGAGGAAGCTTTAAAACTGATTTTGTTGGCTCTTGAGGGAGGAGAAGCTCTGTCTAGGAAagttttagttctttttgttGTTCAGAAGTTGGAGCCACAGTTTCCACAAGCCTCTAAGACAAGTATTGGCCATGTAGTACAGTTACTTTACAGGGCATCATGTTTTAAGGTGGAAAAAAAGAGCAATGAATCATCTTTGATGCAGCTTAAAGAACAGTTCCGAACATATGACGCACTGCGAAAAGAACATGATGCACAGATTGTACAGATTGCTACAGAGGCAGGACTGCGTATTCTTCCAGACCAGTGGTCATCATTGCTGTATGGAGATCTAGATCACAAGTCCCACATGCAATCCATTATCGACAAGcTTCAGTCGCCAGCATCTTTTTCTCAGAGCATCCAGGAGTTGATCATTGCTCTGCAGAGGTCTGGAGACCCAGGTGACCTTTGCCAGATGCGTGACCAGTTTGAGCTGCTCTCACAGATTGATGCTTCACCAGAGGCAGCATGTCCAGAGTGGAAGGAATTAGAGAAAGCAATGGCGTCAGTACATTCTGTTGTTCATGGACTTGTAAAGTTTTCAAAAGCATATGGCAAGGGAATGAGAAGCTCTAGTGATCCACCTCAGCCTCACagcaacaacaaatttaaaaccAGCATGTGCCGAGATCACTCACGAGGAGGATGCCCCAGGGGAGCTCACTGCACATTTGCACACTCTGAGGAGGAGCTAGAGAGGTTCAGCAAGAGGAGAACTCGGGGACCCCGCCCTACAGCAATACCCAGAGGATCGGGCCCTGGGGCAGGGCCTGATCAATACTCCCCTCATGGCTCCATAGAGAATGGCTGTGACACAAGCCCAACTGTTACCCAAGCTCCTGCCAATGCTGTCAATGGTGTGGCCAGATCTTCTCCTCACTATGTTACGGGTGAAATGTCACAATCGACACCCAGTTATGGCCCTCCACCACAAGTAACCCGCAGAGACAGCCAGGAACAAGTTCAGATGATAAGTCAGCGAATGAAGCACATGAACATTTACCAGAGTGATGGCTTTGGGGGGCCTCGCTCGGCATATGATCATGTGCAGCCATCTTATATTCCTTCTTCTGGAAGTGAGAGAGGTGCATATTTCCAGTATTACCCGCCTGGCAATTCCTATTCTAATGTCGTGTCCAGAGGAAAGGATATTACACTTG

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003562 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14634 all species →	zf-RING_5	zinc-RING finger domain	Domain	Interproscan
PF21206 all species →	Roquin_1_2-like_ROQ	Roquin 1/2-like, ROQ domain	Domain	Interproscan
PF18386 all species →	ROQ_II	Roquin II domain	Domain	Interproscan
PF00642 all species →	zf-CCCH	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR048575 all species →	Domain	Roquin 1/2-like, ROQ domain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR041523 all species →	Domain	Roquin II	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR036855 all species →	Homologous_superfamily	Zinc finger, CCCH-type superfamily	Interproscan
IPR052249 all species →	Family	Roquin domain-containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13139 all species →	RING FINGER AND CCCH-TYPE ZINC FINGER DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0000288 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Interproscan
GO:0003725 all species →	Molecular Function	double-stranded RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0010494 all species →	Cellular Component	cytoplasmic stress granule	Interproscan
GO:0035613 all species →	Molecular Function	RNA stem-loop binding	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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
K15690	RC3H; RING finger and CCCH-type zinc finger domain-containing protein	-	Ubiquitin system	ko04121	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 Porites divaricata 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 Porites divaricata, 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 →