Gene detail

Detailed information of ENSVBPP00000022157.1 in Meandrina meandrites

Genomic Location: chr4:7274285...7283626
NR annotation: XP_020620097.1, LOW QUALITY PROTEIN: E3 ubiquitin-protein ligase listerin-like [Orbicella faveolata]
Species Meandrina meandrites · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSVBPT00000023087

ATGATTCTACTTAAAACAGCCGTGCTCATTCAAGAAAAGTTGGAGAAAGTCGAGACTCTCGAGAGAGTGGATAACCTCGCTATCATAGCTGTTCATCTCCTGAAAGATGCCAGTCACTTATCTTCTGAGGAAGAGGAAGGCGAGTCGTTGTCACAGCGAGTTTTCGTGGCCTTGACACCTAGTGAACAGCAGTTGAATTTTCTTAGGAACGAATATTCCACGAGTCAGTGGCTGTTGGATCCGCTTTTGCAAAGAAAACTAACAGTGATGTCCGACTTTCACGACCAGCACGCCGAATGCGAAAATACATGGTCCACTCTTACGAATCATCAGAAAATGATTGTGTTTTCGTCGAGTCTTGTCAGAGAAATCCTCTCAGATTCGAATGAATTGACACCGGGCTTGAAGAGTAAAGTTATAACAAGAGATTGCTTTGTCCGATTGTGGCTGGAGACGAGTTGGGTTCGAGATTGGTACACTTGTGTTTTAGGGTGTAGTGGCATCACAGAGGAATTTGCCGCGTACAGCAGCATTAGTGACCAGGCCGTCTCCAATCTTCTGGTGAAACTCCAACAGACTAGTCACCGTCTCCTAGAGCATATCAAGGAGAAACAGTGGAGCGAAGCTCTTGTTGCAGATGCGCTAACACGTTCACGAACAGAGGGCTTCTTGTGGTGCCTTGTGCTTGGAGATGCCTTAAAAGACTTGCAGGGCGCGGCTTGCGAAACTGCTTTTCTGTTGGCTGAGGTTCAATCTTTAGGGTGTCTAGAAGAAAAGGAATGCCAGGCTCTCAATACTTTGATAGCTCATGTGGACGGTATTTACGAGCTAAAAATCATTACTGAGCAGTATACTAGACTATTACGCGAAGAGAACGACGAAGGTGGCTTTGCTCGGGTGTTGGCTGTTATTAATGGTTCTCTTCACCAGTGGTTCAAACAAACCAAAGACGTTGAGGAAGCCCTGCTTGAGTACCAGCTTACACTAACGGAGATTTTAGACGAGTTGGTAGAGTGGAACAAGACACATGACAACCTTTTGCTCATAAACAGCCCTTTGGATGATGCCTCGATGAGCGTGTTGAGTCTAAACTTATCTCTCATTAGGATTCTTGAAATGGCTGTTCTTCACTGTCCTGACAAGATGAACGGCAAACATTGGGATTTTGTGCTGTGTAGTTTAGCTGGTTGGCTGCAGACCTGCGAGGAAAATCGCTCAATGCTAGCAACTTCATTGAAATGTGTTGCTCTCTGCTGCCAAGTTTGTTCACTCTTCTGCATCGTAGCTCGGTTCTTTCAAGAGAATGCTTCAAAACTCTCCACGATCAGAGACATTGGACTCTCCAGTGAGGCGTCTCATGAAGTAGAGAGCGGATCTTTAGCAACCGCCGACACTGGAGAGTTTCCTCCAAATCTGTTCGCTGAATGGCAGGAATTCTTCAGTGGAAATCTGTTCTATGCAGTGTTGCAGTTGTTCATGCTCCATGCAGCCCAGTGTCAAAGCTTGCATTTTGAAGCCTCACTCTGGTCAAACCGTATCAGTGAGTCACTTGGTAGGGCTGTGATCTACACTCCAACGGCACTTTTAAAGGAGCATAAGTTCCAGGGGCCACCACATGCTACCGCTAACGAATCCTTAAACATGCCCCAGTGGATAGGTGACCTCCTGGAGCACTGCTTGCCTCTTCTAAAATGCAGTCTGCACGGTCTTCAATTTGCTGCCTATCATCTGCTTTCCAAAGTAATGGCGGAGATCACTTTGTTGGATGAAAAGGAGCCCGAGTCCGAGGAAGGAGTTGATGAGCCAGTCAAATCCCCACCCACTCCACTGATAGCCCTGATAAGTACATCGTGCGCACACATGGCTGAGATGGTGAGTGAGGCGCAAGTCCCGTTTGGAGAGCATCTGGACATGTCCAGCGACACGGAGGCGCAGAACGTAAGCCTTGCTCTTATGTTAGCCTGGAAACTTCTGCTTCAGTTTTTTAGAAGCTTAAGGCAAGAAAGACGGGTGGAATACGCCAAGTATATCAGGCAAAACAAGATGGTGGGCAATCTTCTCGGCGTGCTGTTTCGACTGATTCCACTCAAAGCAGTAGCATTGACGGCGACAATGGTAGCAGATGACTTTGAGCCAGAGATCGGACGTTTTGCTGGTCAGCGCACTATCCAGCAGCTAGCATGCGGGCTGTACTATTCCTTGTCACAGTGGATGCCGGCCATTGTGCGACAGTGGTGGAATGGGTTGGATAAGCGCCAGTCAGCTATTGTCGACAAATTCACGACTTCCATTATCACACCTCAACTGTGCCAGCGAGAAATGCAACTGGTTCAAAGCTCGTCAATCCGATTTGACAACATGCAAGTTAAGACTCGACCCAGTGCCCGTGAGGTAGCCGCGGTGTACACGGTTGACGAGATCTCCATGGAACTGGTGGTGAAACTCGCGCCAAACCATCCGCTGGGCGTGGTCTCAGTGGAGAGCGGCAAAAAGATTGGCGTGACGGCCGCTCAGTGGAGGAGCTGGATGCTACAGATGACCACATTTCTCACTCATCAGAATGGAAGTATAATGGATGGCCTCATTCTGTGGAAGCGAAATGTGGACAAGCGTTTTGAGGGAGTAGAGGACTGCATGATCTGTTTCTCTGTGATTCATGGCAGTAATTACTCTCTGCCCAAATTGAGCTGCAAGACTTGCAAAAAGAAATTTCACTCGGCCTGCCTGTACAAATGGTTCAGCACCAGTAATAATGCTACGTGTCCTTTGTGTCGAAATCTCTTCTAA

Transcript

ENSVBPT00000023087

CAACGGTATCGCAGTCCTTGACAGAAACATGGCAAACTGGATTAAAGGTGTTCAAGCATTTACCTTCTGAAGTGGACTGTAATCCGTGTGAAATGATTCTACTTAAAACAGCCGTGCTCATTCAAGAAAAGTTGGAGAAAGTCGAGACTCTCGAGAGAGTGGATAACCTCGCTATCATAGCTGTTCATCTCCTGAAAGATGCCAGTCACTTATCTTCTGAGGAAGAGGAAGGCGAGTCGTTGTCACAGCGAGTTTTCGTGGCCTTGACACCTAGTGAACAGCAGTTGAATTTTCTTAGGAACGAATATTCCACGAGTCAGTGGCTGTTGGATCCGCTTTTGCAAAGAAAACTAACAGTGATGTCCGACTTTCACGACCAGCACGCCGAATGCGAAAATACATGGTCCACTCTTACGAATCATCAGAAAATGATTGTGTTTTCGTCGAGTCTTGTCAGAGAAATCCTCTCAGATTCGAATGAATTGACACCGGGCTTGAAGAGTAAAGTTATAACAAGAGATTGCTTTGTCCGATTGTGGCTGGAGACGAGTTGGGTTCGAGATTGGTACACTTGTGTTTTAGGGTGTAGTGGCATCACAGAGGAATTTGCCGCGTACAGCAGCATTAGTGACCAGGCCGTCTCCAATCTTCTGGTGAAACTCCAACAGACTAGTCACCGTCTCCTAGAGCATATCAAGGAGAAACAGTGGAGCGAAGCTCTTGTTGCAGATGCGCTAACACGTTCACGAACAGAGGGCTTCTTGTGGTGCCTTGTGCTTGGAGATGCCTTAAAAGACTTGCAGGGCGCGGCTTGCGAAACTGCTTTTCTGTTGGCTGAGGTTCAATCTTTAGGGTGTCTAGAAGAAAAGGAATGCCAGGCTCTCAATACTTTGATAGCTCATGTGGACGGTATTTACGAGCTAAAAATCATTACTGAGCAGTATACTAGACTATTACGCGAAGAGAACGACGAAGGTGGCTTTGCTCGGGTGTTGGCTGTTATTAATGGTTCTCTTCACCAGTGGTTCAAACAAACCAAAGACGTTGAGGAAGCCCTGCTTGAGTACCAGCTTACACTAACGGAGATTTTAGACGAGTTGGTAGAGTGGAACAAGACACATGACAACCTTTTGCTCATAAACAGCCCTTTGGATGATGCCTCGATGAGCGTGTTGAGTCTAAACTTATCTCTCATTAGGATTCTTGAAATGGCTGTTCTTCACTGTCCTGACAAGATGAACGGCAAACATTGGGATTTTGTGCTGTGTAGTTTAGCTGGTTGGCTGCAGACCTGCGAGGAAAATCGCTCAATGCTAGCAACTTCATTGAAATGTGTTGCTCTCTGCTGCCAAGTTTGTTCACTCTTCTGCATCGTAGCTCGGTTCTTTCAAGAGAATGCTTCAAAACTCTCCACGATCAGAGACATTGGACTCTCCAGTGAGGCGTCTCATGAAGTAGAGAGCGGATCTTTAGCAACCGCCGACACTGGAGAGTTTCCTCCAAATCTGTTCGCTGAATGGCAGGAATTCTTCAGTGGAAATCTGTTCTATGCAGTGTTGCAGTTGTTCATGCTCCATGCAGCCCAGTGTCAAAGCTTGCATTTTGAAGCCTCACTCTGGTCAAACCGTATCAGTGAGTCACTTGGTAGGGCTGTGATCTACACTCCAACGGCACTTTTAAAGGAGCATAAGTTCCAGGGGCCACCACATGCTACCGCTAACGAATCCTTAAACATGCCCCAGTGGATAGGTGACCTCCTGGAGCACTGCTTGCCTCTTCTAAAATGCAGTCTGCACGGTCTTCAATTTGCTGCCTATCATCTGCTTTCCAAAGTAATGGCGGAGATCACTTTGTTGGATGAAAAGGAGCCCGAGTCCGAGGAAGGAGTTGATGAGCCAGTCAAATCCCCACCCACTCCACTGATAGCCCTGATAAGTACATCGTGCGCACACATGGCTGAGATGGTGAGTGAGGCGCAAGTCCCGTTTGGAGAGCATCTGGACATGTCCAGCGACACGGAGGCGCAGAACGTAAGCCTTGCTCTTATGTTAGCCTGGAAACTTCTGCTTCAGTTTTTTAGAAGCTTAAGGCAAGAAAGACGGGTGGAATACGCCAAGTATATCAGGCAAAACAAGATGGTGGGCAATCTTCTCGGCGTGCTGTTTCGACTGATTCCACTCAAAGCAGTAGCATTGACGGCGACAATGGTAGCAGATGACTTTGAGCCAGAGATCGGACGTTTTGCTGGTCAGCGCACTATCCAGCAGCTAGCATGCGGGCTGTACTATTCCTTGTCACAGTGGATGCCGGCCATTGTGCGACAGTGGTGGAATGGGTTGGATAAGCGCCAGTCAGCTATTGTCGACAAATTCACGACTTCCATTATCACACCTCAACTGTGCCAGCGAGAAATGCAACTGGTTCAAAGCTCGTCAATCCGATTTGACAACATGCAAGTTAAGACTCGACCCAGTGCCCGTGAGGTAGCCGCGGTGTACACGGTTGACGAGATCTCCATGGAACTGGTGGTGAAACTCGCGCCAAACCATCCGCTGGGCGTGGTCTCAGTGGAGAGCGGCAAAAAGATTGGCGTGACGGCCGCTCAGTGGAGGAGCTGGATGCTACAGATGACCACATTTCTCACTCATCAGAATGGAAGTATAATGGATGGCCTCATTCTGTGGAAGCGAAATGTGGACAAGCGTTTTGAGGGAGTAGAGGACTGCATGATCTGTTTCTCTGTGATTCATGGCAGTAATTACTCTCTGCCCAAATTGAGCTGCAAGACTTGCAAAAAGAAATTTCACTCGGCCTGCCTGTACAAATGGTTCAGCACCAGTAATAATGCTACGTGTCCTTTGTGTCGAAATCTCTTCTAACACTAAGTGATCAAGATCGGATTTCTCCCCAGAATTACTATATATTGTCTGTCAGAGAGGTTACGAGAATAACGAAATTCATCAGCAAGGAGCCATAGTCTTGATCTCTcaacaaattctcagaactaagCCAAAAACAAATGTATGACAATCGGTAATGGGAATTTCTCTGTTGGCATCGGCTATGTTATACGTGGTGTGAAGACAGGTGCAAGCATTGCCTCgcccaatctcgtccccagagggcgcgatccttctggactgcgccaggaatcgagacctctgggctaatCTGAAAGCTCGCCATGAAGGCGaccgaatctgattggctgttgaaaacttGTTCGTTTCATCACAATCTCAGGTGCACGCGcacaatcaaaccggaaccaggattttctggttccggttttggattcgtcCAGAGCCGTTGAGTtttccgaccgctggtcaaggggaacgCAGGCTATGGGAACGAGATTGTGCATCGCCTCTTTCCTCCGCAGAGGTAAACTGGAGAGGCCTCTGCTGCGGAGAGAGTCGCATCGCAGCTTTGATGTGGTGATTCGAAACCAAGCACAGAGAAGCAAATAAAAACGCGTTAACATCGTAAAAATATTATGCGCGTTTTCAAGTACTGTAAGGGAAAAGAAGGTTGAAGCTTGATGGAAAACTGTGAAATGCTCTTGCATAATAGCAAACGTTAACCCGGCGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O94822	E3 ubiquitin-protein ligase listerin OS=Homo sapiens OX=9606 GN=LTN1 PE=1 SV=6
Q6A009	E3 ubiquitin-protein ligase listerin OS=Mus musculus OX=10090 GN=Ltn1 PE=1 SV=3
E1C231	E3 ubiquitin-protein ligase listerin OS=Gallus gallus OX=9031 GN=LTN1 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003780 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13639 all species →	zf-RING_2	Ring finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039795 all species →	Family	E3 ubiquitin-protein ligase listerin	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR011016 all species →	Domain	Zinc finger, RING-CH-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR039804 all species →	Domain	Listerin, zinc finger, RING-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12389 all species →	ZINC FINGER PROTEIN 294	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0043023 all species →	Molecular Function	ribosomal large subunit binding	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0072344 all species →	Biological Process	rescue of stalled ribosome	Interproscan
GO:1990112 all species →	Cellular Component	RQC complex	Interproscan
GO:1990116 all species →	Biological Process	ribosome-associated ubiquitin-dependent protein catabolic process	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
K22377	LTN1; E3 ubiquitin-protein ligase listerin	EC:2.3.2.27	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 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 →