Gene detail

Detailed information of ENSVBPP00000024317.1 in Meandrina meandrites

Genomic Location: chr4:4195107...4208070
NR annotation: XP_020622869.1, E3 ubiquitin-protein ligase parkin-like [Orbicella faveolata]
Species Meandrina meandrites · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSVBPT00000025343

GTAAGTGTTTTTGATAGTTGACGATGGCAGCAAGGAGACCTCAAAAGGTTGCTATCTTTGTGCGGCTTAACTCTAACACAAACATACCAGTACAAATAGATCTTCAGTGGAATGTGTTAAAGTTAAAGCAGGAAATAGCTGCCAAACAAGGGGTGGATCCCACCGAGATACGAATCATTTTTGCTGGTCGAGAACTAAAGGATGACCTCCAGTTGAAGGATGCGGAGATCCCCAACCAAAGTGTTATCCATGCTGTTCGTGGTGGCCGTTGGTCAGCAAGACCAGCAAGGGGAAAGACAACACCATTGAACCAAGTTAAACTTGCTACTGTTGGAGAAGAGGAGGAGGATGCAGCAAGCTCAGTAGCTGGAGCATCTGCTCAGCGACAAGCTCAGTATTTTGTTTATTGCAAGACTTGTAAGTTAGTGACCCCAGGAAAGTTGAGGGTCCGTtgttcaatttgcaaagaaggAGCAATGGTTCTTCAGCAGGACCCCAGCAGTTGGGAAGATGTATTAAAAACAGGGAGAATAAGAGGTTCCTGCAAAACTCCAGGATGTGAAGGAGCCGTAGCGGAATTTTActtcaaatgcgcattacacCCTGCTGCTGAAGGCGACAGATGTGTGGCACTCAATTTGATACGATCAAACACAAGGGATATTCCTTGTTTGGCATGCACAGATGTCAAGGACACTGTTCTGGTATTTCCGTGTGCGGATGGACATGCCGTGTGCCTGGATTGCTTTGAAATCTACTGCACAACTAAACTGAACGACAGACAGTTTGTGCATAGTGAGACTTACGGTTACACTTTACCGTGCCCGGGCAGTTCAGGTAGCTGCACCACCGCCCTCATTTCAGAGGCTCATCATTTCCGGGTACTCGGAGAAGACCAGTATGACCGTTATCACAGGTTTGGAACTGAAGAATTTGTTCTGAATAGCGGCGGTGTGTTGTGCCCAGGCCGCGGCTGCGGAATGGGACTGTTGCCAGAGCCGGACATGCGCCGTGTTAAGTGTGATGGGTGTAAGCTGGAGTTCTGTAAAGAATGCAAGGAACCCTTTCGACGAGGTCACTCGTGCAATCAAAACCAGTCAAATGCCGCAACTGCCGCTCGACCTAGTAATTACCGAGTAAACGCTGATAACGCCAGACGAGCGCGTTGGGAGGCTGAGGCCAAACAGGTGATTAAACAGATCAGCAAGAAGTGTCCCGGATGTAGGATAAACACGGAGAAAAATGGTGGATGTAACCACATGACCTGCACTCGATGTAAGTTTGAGTGGTGCTGGATTTGCCTTATTGCTTGGAACCCAGATTGCCAGGGATCCCATTGGTTCATACAGCGCTAGTGCGATATACCTTGTCACAGTATCTCGTGTTCGCGACAGCTGCTAGTTTACCTTCCCATGTAGACATTCTTTTGTTAGTCACGCAATCTCGTACGGCAAAGATTGTGTGACAGGCATAAGGCTGGTGTTAGCTCAAAGCGACcgcgaaatttttttttttaaaaaaaaagctatGTAGTGAAGTATGGTGTTAGAGATCGATGCAAAGACGAGAGGAGTTTTGAATTAAATTGTTTTAGTTAAGTCCCAGCTTGGGTATATATTCTTAGCctcaacattcttataaaaaacgTGGCTTTTTTACCCGTGCGACGCATCGGCGGCCGTTGTGCATACTCGTCTGTCCCGCGCAGTAAACAATGCACGCAGTGCTGAAAAACAAattggccgaaatatccgaaaagaaaaaaaatttaaatgggCGATGGATGTGAGCTTGCATGTCTCAATTTTCTGagcttttcattttaaaagttCTGGCTTGAACGTTTGATTTTTGCTTTTATGATAttagtttaatttttgtttggccGACTGGAATCGTTCCGCACTGCGTGCATTGTTAGACGAGTAACCTGAGCGGCCGTCAAATCAAGCCACTGAATTAACTGTTTACCGATTGGGCAGAAtactgctcaatcaggagccagcattcacagagccgtttggaaatggtctggagagactcgtttcccaggggcccTTTCCGcccttcttgaaaactttcggcAACTTCTCGTATTTCAAGCAACTCTTTGTATTCTGAGCAACTTCAAGACCGAAGATTGTCCGAGTGTTGTTTGAAGGCCATACGAACGTCTCTGAGCATCTTTCGAAAGTTGCCGAAAATGAACGAAGTTTACCGAACAACTCCGAGGGAGTTTCGAAGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9WVS6	E3 ubiquitin-protein ligase parkin OS=Mus musculus OX=10090 GN=Prkn PE=1 SV=1
O60260	E3 ubiquitin-protein ligase parkin OS=Homo sapiens OX=9606 GN=PRKN PE=1 SV=2
Q9JK66	E3 ubiquitin-protein ligase parkin OS=Rattus norvegicus OX=10116 GN=Prkn PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002516 (this species only) · gene tree & orthology
Ubiquitin family	ULD\|UBL\|NEDD8 · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_Other · all ubiquitin genes in this species
Ubiquitin family	ULD\|UFD/UBQ\|UBQ_PIM · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity\|RBR · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17978 all species →	zf-RING_14	RING/Ubox like zinc-binding domain	Domain	Interproscan
PF00240 all species →	ubiquitin	Ubiquitin family	Domain	Interproscan
PF17976 all species →	zf-RING_12	RING/Ubox like zinc-binding domain	Domain	Interproscan
PF01485 all species →	IBR	IBR domain, a half RING-finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR047536 all species →	Domain	E3 ubiquitin-protein ligase parkin, Rcat domain	Interproscan
IPR000626 all species →	Domain	Ubiquitin-like domain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR031127 all species →	Family	E3 ubiquitin ligase RBR family	Interproscan
IPR047535 all species →	Domain	E3 ubiquitin-protein ligase parkin, RING finger, HC subclass	Interproscan
IPR003977 all species →	Family	E3 ubiquitin-protein ligase parkin	Interproscan
IPR041170 all species →	Domain	RING/Ubox-like zinc-binding domain	Interproscan
IPR047534 all species →	Domain	E3 ubiquitin-protein ligase parkin, BRcat domain	Interproscan
IPR002867 all species →	Domain	IBR domain	Interproscan
IPR041565 all species →	Domain	Parkin, RING/Ubox like zinc-binding domain	Interproscan
IPR029071 all species →	Homologous_superfamily	Ubiquitin-like domain superfamily	Interproscan
IPR044066 all species →	Domain	TRIAD supradomain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11685 all species →	RBR FAMILY RING FINGER AND IBR DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0000422 all species →	Biological Process	autophagy of mitochondrion	Interproscan
GO:0001933 all species →	Biological Process	negative regulation of protein phosphorylation	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0005794 all species →	Cellular Component	Golgi apparatus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0010821 all species →	Biological Process	regulation of mitochondrion organization	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0031624 all species →	Molecular Function	ubiquitin conjugating enzyme binding	Interproscan
GO:0032436 all species →	Biological Process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0042981 all species →	Biological Process	regulation of apoptotic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:1900407 all species →	Biological Process	regulation of cellular response to oxidative stress	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion 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
K04556	PARK2; parkin	EC:2.3.2.31	Mitochondrial biogenesis	ko03029	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 Meandrina meandrites 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 Meandrina meandrites, 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 →