Gene detail

Detailed information of ENSLDHP00000038417.1 in Eunicella cavolini

Genomic Location: chr5:34111479...34131821
NR annotation: CAB3985904.1, thrombospondin-3 isoform X2 [Paramuricea clavata]
Species Eunicella cavolini · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSLDHT00000041794

ATGCCACTGTTTGCTATCACTTCTGTCTTGTTGACGATATTCACATGTCAGGGTTACGAGATCAGTCTTTTAACGACGTTACTGGATGATCCTGGAGAGTATAATGTGGAGCTGGACAGTGGAATCAACCACCGTTCTGATGCCTTCAAATTCACTTCGATCGTCAAGAAACTTTCCTTGCCTTTTGAACTGTCGTCTGAAATTATCACACACATGGATGCCCACGATGCTCTGATCCTCGTCGTCAACCTGAAGATTGATCCGTACAACTACGGAACCGTGTTCTCTGCCAGTGGAAACACCAAGGAAGTTTTGTTCGATGTCTGGGTCAAAAGTGGGGTGAATCCCGCGGTCGGATTGCGGTACGCGCCTATAAACTCATCCAAGATCGAAACGGTCAGTTTTGGTCCAGTCTCAGACTTCAGGTTCAAACGATGGAATAAAGTTGTGCTTCATGTATACAGGGTGGGAGTGTTTCAATCAGTTGTCGATGCTTACGTCAACTGCGAGAAAATTGGACGCAAGATAACGCGAAGTGTTTTAGATTTGTTTGTTTACAAGAAGAAATTCAAGCCTAACAAAGTAGAGTTTCGTATTGCACAGAGAGGTTATGGAAGAAACGTACACTCAAGATATTTAGGATCCATGCAAGATTTACGGCTGGTCTTCAAGAGAGAGATTGACACATTTGTTGACAAAGATTTGTGCAAGTATCCATTTGAAGAGAAGAATGAGTTTATACTCTCATATCATCGCGCAATGGGTGAACCAATCAGAACAGATTATGGCTCTGAACCAGCAATGACTGAACTAATGAGCATGATCAAGGATTTACGATATGATTTAACTGTCCAGACAGCGGAAATGAAATATGTGAGGCAACTTGTGGAAGGCTGTCAGCTCTGCAGAGTAACGGACTTCTGTGCCATGAGACCGTGCTTTCCCGGCGTACAATGCTTCAATGCTCCAAAATCTAAGGATGGATTTTACTGTGGTAATTGTCCATTTGGTAGCCATGGCGACGGAATACATTGCAGTGACATTGATGAGTGTGACTATCACCCATGTTCAGTGCTCTCAACTTGCATCAACAAAAGTCCTGGTTACACATGCGAGGGTTGCCCAGCCGGCTATACCGGACCTGTCCCGAGTGGTATCGGAGTTGCACACGCTGCAAGAACGAAACAGATTTGTGCGGACATTAACGAGTGTGAAATGGACAACGGTGGATGTGATAAACTTGTGAAATGCATAAACACGCTGGGTAGTTTTGAATGTGAGTCGTGTCCACCGGGGTACGAAGGGGATTCAAAGATCGGGTGTCGTTTCCAACAATACTGTGACCCTCAGAATCCCAAGAGTAACCCATGCAACAAATTTGCCAAGTGTATCCCGTTGAATGATGGGAAGGATTACAAATGTGAATGCTTTATTGGTTTTGCTGGAGATGGGTTCACTTGTGGATATGATAGGGATGCTGATGGATACCCCGATCAAGATCTTGACTGTAAAGATAAAGATGAATATTGTGTAAAGGATAACTGTCCGTATCGGCCGAATCCAGACCAGAATGACAAAGATGGCGACAGTGTCGGAGATGTGTGTGACGAGGACATTGATAACGACAGAGTCAGCAATGAACAGGACAACTGTCCCTGGGTCCCTAACAGAGGTCAATATGACTTTGATAAAGATGGATTTGGCAACTTGTGTGATAACTGTCCTGCTGTAAAGAATCCAACTCAAGAAGActttgatgatgatggtgaaggTGATGAATGCGATCAAGACAAGGATGGAGATGGTTACGACAATGATAAAGACAACTGTCCAATGGTCTATAATGTCAAGCAGAAAGATACAGATTCGGACGGCATAGGGGACCCATGTGATAATTGTCCATTAGCACGCAATCCCAACCAACGTGACAAAGATGCTGACTTTATTGGAGACAAATGTGACACGAATGTTGACAGGGATAATGATGGTGTCGAAGACACTGTTGATAATTGTCCACTTGTTAGTAATCCAGAACAAAGAGACGCTGATGTCGATGGTGTAGGCGATGTTTGTGATGAAGATGACGATAATGATTCAATATTTGATGCTGCGGACAATTGTCcattagttgccaataaaaaccAGACGGACAGCGATGGCTCCGGGATCGGGGATGTGTGTAAAGGGGACTGGGATGGAGACGGAGTCCCGGATGAGTATGACGCAAGCAAGAATAACAATAAGATAACATTCACGGACTTCAGAAGACTACAGAGTGTAAATCTTGATGTGAAAAAGGCTACACAGGCTAATACTATTTGGGTTGTTACGAAGAAGGGAACAGAAGTGAGACAAACAGCTAACAGTGACCCTGGAGTTGCCGTCGGCCAGGACAGATTCGCTGGAGTAGATTTCAATGGTACGATGTATGTCGATACGAAATCTGATGATGACTTTATTGGTTTTGTGTTCAGTTACCAAGATAGCTCTTCATTTTATGCCGTCACTTGGAAAAGAACTGAACAAGTCTACTGGGTGGAGAATCCTTTTAGAGCCATTGGTATTTCTGGACTTCAATTAAAGAAAGTCAGATCATCTTCAGGTCCAGGTCACGGCTTACGTAACGCTCTCTGGCACAGAGGAAGCACTCCAAATGAGGTTGAGTTGTTATGGTCAGACGTCAGACAAGCAGGGTGGGAGCCACACGTTCGTTATAATTGGCAGTTAATACATCGGCCTGAACATGGTTTGATTAGGTTAAAGTTCTTCAAAGGCAGGCGGGAGTTTGCAGATACTGGATATATTCATGATAGCAGTTTTGCTGGGGGTAGAATGGGTCTGTATGTATTTTCTCAAGCTGAGGTTGTATGGAGTGACTTGTCTTATCGAGCTAATGATGATCTACCTGAAGACTACGATAACACGAAAAGATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8JHW2	Thrombospondin-3a OS=Danio rerio OX=7955 GN=thbs3a PE=2 SV=2
P49746	Thrombospondin-3 OS=Homo sapiens OX=9606 GN=THBS3 PE=1 SV=1
Q9Z1T2	Thrombospondin-4 OS=Mus musculus OX=10090 GN=Thbs4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000885 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07645 all species →	EGF_CA	Calcium-binding EGF domain	Domain	Interproscan
PF11598 all species →	COMP	Cartilage oligomeric matrix protein	Family	Interproscan
PF02412 all species →	TSP_3	Thrombospondin type 3 repeat	Domain	Interproscan
PF05735 all species →	TSP_C	Thrombospondin C-terminal region	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR028974 all species →	Homologous_superfamily	TSP type-3 repeat	Interproscan
IPR049883 all species →	Domain	NOTCH1 EGF-like calcium-binding domain	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan
IPR017897 all species →	Repeat	Thrombospondin, type 3 repeat	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan
IPR024665 all species →	Domain	Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain	Interproscan
IPR008859 all species →	Domain	Thrombospondin, C-terminal	Interproscan
IPR018097 all species →	Conserved_site	EGF-like calcium-binding, conserved site	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR003367 all species →	Repeat	Thrombospondin, type 3-like repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10199 all species →	THROMBOSPONDIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0062023 all species →	Cellular Component	collagen-containing extracellular matrix	Interproscan
GO:0005576 all species →	Cellular Component	extracellular region	Interproscan
GO:0007155 all species →	Biological Process	cell adhesion	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 ENSLDHP00000038417.1.

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 Eunicella cavolini 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 Eunicella cavolini, 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 →