Gene detail

Detailed information of ENSBQFP00000042002 in Heliopora coerulea

Genomic Location: JASJOG010000232.1:256895...281558
NR annotation: XP_028409678.1, calpain-B-like [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSBQFT00000047245

ATGCCTTACAAGCAAAGTTTTGAAGAGATCAAGGCGGCATGTCTGCGGTCGGGAAGATTGTACGAAGACCCCGACTTCGAGGCAATCGACGATAATGTATTTACAAGCCGTCGTCCACCTCGACCATTCGTGTGGCGTCGTCCTACGGAAATGGTTAAAGATCCAGTTCTAGTTGATGCAGGTGCCAGCCGAATGGATGTTGCTCAAGGTCGCTTGGGAGATTGTTGGTTCTTAGCAGGAATTGCTTCCCTTACCCAACATAAAGCCCTTTTTGAAAGAGTAGTGTCTGTTCATGATCAGAGTTTTGGCAAAGACTACTGTGGTGCCTTCCATTTTTGTTTCTGGCAAGGTGGTGAATGGGTGGATGTTGTGATTGATGATCGCCTACCAACCATCAACAACCAATTGATATTTGTGCATTCTAAGTCAAGAAATGAATTCTGGAGTGCCTTAATGGAAAAGGCTTATGCCAAACTGTGTGGCTCCTATGAAGCTTTGAAAGGAGGACAAACAAGTGAAGCAATGGAAGATTTCACAGGAGGAGTGACTGAGTCATTTGATCTTGGTTCCAAAGCACCCAACAACctgtttcagattatgaccaAAGCAATTGAAAGGCAATCTCTCATGGGCTGTAGCATTAATGCCAAACCAAACCAGATCGAAGCCAAGTTGGATAATGGTTTAGTTATGGGACATGCATACACTGTAACTGGAGCAAGAAAGGTGACTGCCAGGACTAGGTCTGGAAGGATGGAAGTTGAGCTAGTCAGAGTGCGAAACCCTTGGGGAAATGACAGAGAGTGGAAAGGACCCTGGGGTGACAAGTCTCCTGAATGGACTCTGTTGTCTGATGCCGAGAAGAGAGAAATGGAGTTGACCTTTGAAGATGACGGAGAGTTCTGGATGAGCTATCGGGACTTTATAACACATTTCCAACGACTGGAAATTTGCATGTTGAGCCCAGACGGAGCAACTTTCGACGATAATCAGAAGAGGGCCTGGGAGATGGCTCTGCATAAAGACAAGTGGAGGATTGGAAGTACAGCAGGCGGTTGTCGTAACAACCCTAATACTTTCCACAGAAATCCTCAGTTCAGgGTCACCCTCCAGGACGTGGATGAAGATGATAACGAAGACGTTTGCACGCTCATCGTGAGCTTGATGCAAATTGGTCGTCGAAAGCTGCGAAGGAAGCTTGGTGCTAACTCCAACCTCACGATTGGATTTGCCATCTACAAGCTTGAAGAAGACGACTTAAGGGTTTCCCGTCTGGACAGGGACTATTTCTTGTACCATGCCTCCACGGCCCGCTCAAACACATTCATCAATGCTCGAGAGATCACCAATCGGTTCCGTCTCAAGCCAGGCGTCTACTGCATCGTGCCGTCTACTTTCGATGCCAATGAAGAAGGAGACTTCTTGGTGAGGCTGTTCTCTGAGAAAGAACACCCAAGCGATGTTCAGGACGAGAAGACGAGAATAACCCGTCCTGTCAAGccgAGAATAACAGCAAGCGAAGATCAAGCTATGGATCGCAAATATAGAGTATTCTTTGAGAAAGTTGCGGGAACGGATGATCAAATTGATGCATATGAATTGAAGAAGGTTTTGGAGGCAGCATTCTCGAAAGATGTTGGTGATAATGATTTCAACATTGAGACATGCAGgaGCTTGATCGCCATGTATGATGACAATGGGACAGGAAAACTTGAGTTTGATGAATTCAAACAGACATTGGTGACAGTCAAAAAATGCCatGCTGAATTCAAGAAATACGATGTGGACGGGAGTGGGGACATGAGCATGTATGAGTTACAAGATGTCATGGAAGCCTTGGGAATCAAGATGAGTACCCGTTGTTTGACTGCGATCACTTGCCGATTTTCCAACAAGAAGGGAGCCGTGGACTTCGACGACTTTTTACAGATTTATACGAGACTTGTGGGCCTCATTGAGACCTTCGAGAAGCACAAGGATGGCCGAAACAGGGCTGTTTTTGATCTTGATGAGTTTATTGAAAGTGCTGCTGGATTATAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9VT65	Calpain-B OS=Drosophila melanogaster OX=7227 GN=CalpB PE=1 SV=2
O35920	Calpain-9 OS=Rattus norvegicus OX=10116 GN=Capn9 PE=2 SV=2
Q9D805	Calpain-9 OS=Mus musculus OX=10090 GN=Capn9 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000855 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01067 all species →	Calpain_III	Calpain large subunit, domain III	Domain	Interproscan
PF00648 all species →	Peptidase_C2	Calpain family cysteine protease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR022682 all species →	Domain	Peptidase C2, calpain, large subunit, domain III	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR022683 all species →	Domain	Peptidase C2, calpain, domain III	Interproscan
IPR001300 all species →	Domain	Peptidase C2, calpain, catalytic domain	Interproscan
IPR022684 all species →	Family	Peptidase C2, calpain family	Interproscan
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR000169 all species →	Active_site	Cysteine peptidase, cysteine active site	Interproscan
IPR033883 all species →	Domain	Calpain subdomain III	Interproscan
IPR050420 all species →	Family	Calpain	Interproscan
IPR038765 all species →	Homologous_superfamily	Papain-like cysteine peptidase superfamily	Interproscan
IPR036213 all species →	Homologous_superfamily	Calpain large subunit, domain III superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10183 all species →	CALPAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004198 all species →	Molecular Function	calcium-dependent cysteine-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K08578	CAPN9; calpain-9	EC:3.4.22.-	Peptidases and inhibitors	ko01002	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000042002 across 37 RNA-seq samples of Heliopora coerulea. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

37Samples

37TPM > 0

6Conditions

670.5Max TPM

360.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	239.42	339.82
polyp and skeleton · 31C, 3week	6	6	410.07	652.95
polyp and skeleton · 28C, 3week	6	6	521.07	670.47
polyp and skeleton · 26C, 3week	4	4	451.75	546.07
polyp and skeleton · 28C, 24hr	2	2	407.97	426.44
polyp and skeleton · 31C, 24hr	2	2	534.14	589.80

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	339.82
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	291.87
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	286.58
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	276.60
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	275.08
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	270.44
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	268.55
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	257.41
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	256.61
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	238.84
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	197.40
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	195.70
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	193.67
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	191.54
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	190.11
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	174.94
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	164.94
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	652.95
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	489.22
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	387.39
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	326.40
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	322.47
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	282.03
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	670.47
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	559.49
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	552.49
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	524.54
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	451.69
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	367.76
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	546.07
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	479.75
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	410.32
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	370.85
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	426.44
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	389.50
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	589.80
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	478.48

Source: CnidoSite RNA-seq expression matrices (HCOER_TPM, StringTie quantification over 37 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Heliopora coerulea 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	27	ENSBQFP00000023423	0.917373402309007
Negatively correlated	430	ENSBQFP00000032499	-0.840972772559092

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, 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.	ready	open →
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 →