Gene detail

Detailed information of ENSAVKP00000018754.1 in Catalaphyllia jardinei

Genomic Location: chr2:38488194...38496607
NR annotation: XP_020627093.1, vesicular integral-membrane protein VIP36-like [Orbicella faveolata]
Species Catalaphyllia jardinei · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSAVKT00000020104

ATTTCGACAAAATTGCTATAATTTTCTTTGCTTAagtatagtaataataaaatatctGGAAAGCTCAAAAATGCTAAAATGTTTTCGGAAGAAAATAACTCACTTTTACCCTACCCTAGAGTAAACATCCATGTCCCATTGAAGCGAGTCTGCAGAGTAACGTCGAGTAACGTAGTAAAGAAAATTTAGCAATGGAGTTCAGGAACGTTTTCTTGTCGCTTTTCTTCCTGTTTATTTCGAAAGTATTAGCGATTGAGGAGCCAAGAGGATATCTTCGAAGAGAGCACTCAATTTTTAAAGGTGCTGGACCTTCAATTCCTTATTGGGATTTCCATGGAAGTACATTTATATCAAGTAGCTACATTAGATTAACGCCTGATCATCAGAGCAAGAAGGGTGGCCTTTGGAATAGTGTGCCATGCCATGTTAAAGACTGGGAGATGTTGCTTCATTTTAAAGTACATGGTCTTGGTGATGTACTCTTTGGTGATGGATTTTCATTTTGGTATACCAGGGAAAGGATGCAAGAAGGCGATGTGTTTGGTAGCAAGGATCATTTTTATGGTCTTGGGATATTCTTTGACACCTACAGTAATCACAATGGCGAACACCAACATGAGCACCCTTACATTTCTGCGATGATTGGAAATGGCTCTGTTCATTATGATCATGATCGAGATGGAACACTAAGTCAAGTGGCTGGCTGCTCAGCAAATTTCCGTGGGAGAGGTCATGATACTTATGCTCTGATCCGTTACTCAGGGACAAAGAACCGTCTTACTTTGTTAGTCGACATTGACAACAAGAATGAGTGGCGCGATTGTTTTGATGTGAGTGGAGTTGAACTGCCCACTGGATTGTATTTTGGAGCATCAGCAGCCACTGGTCAACTTGCAGACAATCACGACATAATATCCATGAAATTATATGAAACTGAAATTCCAGTCACGGAAACTGACGATGAAAGCGGTGTTGATCGCTCAAGAATTGTGCCTGTCGCAACTGGAGCTGAACCGTACAGAGAGCGTGTTGAGGACGTGCAAGGCAGTTTCTCATCAAGGACTGTCAAGGTTTTTACGTGGCTCTTCTGGTTTGCTCTTGTTGCTTGCTGTGTTATCGGAGTTTCTCTCTACATCTACCAGAAACGCCAAGAAGATTCCAGGAAACGGTTTTACTAAGACAGACAGGAACGAACGTTCAAGATACTTCAACGTGATCCAGTCCGAGTGAACAATACCTTCTGTTTTCGTGCGCTCAAGATCGGAGAGAAATGTCTGTTTACTCGGACAGATTTAATTAGGAAGGGTATTTGTTGAACAATTATCACTGGGAACTTCTGTCACTACAGACATTGTGTGCTTGAGGTCTGGAACAAGAACAAGTTTTGGTAAATTCTTGATATAAAACTACCCAAAGTGAAAGAGGTTGTTTATGTTAGTTCTATTTCGTATATTGTGTTGTCTGGACTGCGCAATGCCACaaatcaaagacaaaaaaagttGTTCTCACACTAAGGaatcgtccacactacaccagaggaatttgaaaacgcagtgCGTAACGAGAACGGAAAACATtcgatgcgttttcagagtcaaaacttcgttttcaaaatcctCCGGTGAAGTGTGTTTGGGCCTAGTACAACTGCAATACaatggaacctcgatttaacgaacctctaaATAACGAAGTCCCCAGTAAAAAGAACGATACTCTTTGCCCCAGAAAAAGTAAAGTATATGTTAAAGGAGCTCGATGTAACGAAACCTGGTTACATTGAACATAATTTGCCAGTTCCTTCGCTCTTTGGTATATCGAGGTTCCACTGAACATAACTTAAGACACATTTGGAGGGTGGGGTGGGGTAAATAGACGGCCAAATGACTATTTTCTCATATCAATATCCCAAATTCACTACCGTCATCATTTATGTATGTGTGATTACGTGCGAAGTGGAGCAAACTAAAAGACAGTGTGAGCACAATTAGTCACTGAGACCAGAATGTGTTCACCTTCACTT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q12907	Vesicular integral-membrane protein VIP36 OS=Homo sapiens OX=9606 GN=LMAN2 PE=1 SV=1
P49256	Vesicular integral-membrane protein VIP36 OS=Canis lupus familiaris OX=9615 GN=LMAN2 PE=1 SV=1
Q9DBH5	Vesicular integral-membrane protein VIP36 OS=Mus musculus OX=10090 GN=Lman2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006619 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03388 all species →	Lectin_leg-like	Legume-like lectin family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051136 all species →	Family	Intracellular Lectin and Glycoprotein Transporter	Interproscan
IPR005052 all species →	Domain	Legume-like lectin	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12223 all species →	VESICULAR MANNOSE-BINDING LECTIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000139 all species →	Cellular Component	Golgi membrane	Interproscan
GO:0005537 all species →	Molecular Function	D-mannose binding	Interproscan
GO:0005789 all species →	Cellular Component	endoplasmic reticulum membrane	Interproscan
GO:0005793 all species →	Cellular Component	endoplasmic reticulum-Golgi intermediate compartment	Interproscan
GO:0006888 all species →	Biological Process	endoplasmic reticulum to Golgi vesicle-mediated transport	Interproscan
GO:0030134 all species →	Cellular Component	COPII-coated ER to Golgi transport vesicle	Interproscan
GO:0016020 all species →	Cellular Component	membrane	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
K10082	LMAN2, VIP36; lectin, mannose-binding 2	-	Lectins	ko04091	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 Catalaphyllia jardinei 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 Catalaphyllia jardinei, 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 →