Gene detail

Detailed information of ENSBQFP00000016450.1 in Heliopora coerulea

Genomic Location: JASJOG010000036.1:914685...948622
NR annotation: XP_028393631.1, semaphorin-5A-like isoform X3 [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSBQFT00000018376

ATGCACAGATGTGATACGCTTCGAATGGAAGATCTTGTGATTGCTTACACGTTTGTTTTTCATCGAGTTGTTGATAAGCACAAGCTAACGAAGACCATGTGCGCTCAAATGTCTTTGTATAAATTCTTGTTGGTCACTCAGTGGCTGCTCTTCAGCAAAGCAACCACGAATGAATTGATAAAACGAAGGAGCTACGAACAGAAGCTGCATGTTGTTTCTCTATACGAAGagTTAAATTTGGAGGAGTTTAGTTCCAGCTTTTCTGGAAATTATACAACTTTGTTTTTTATGAAGAAAACTCTTTTGGTCGGAGCCAGAAATTTCCTTTTAATATTCAACACAACAAATGGCCTTGAAATCATTAAGAATATAAGCTGGATACCTAAAGAATCTATTTTGCAAACGTCTTGTGTACAATCTGGTATCCCGCAGGATGAGTGTTTTAACTTTGTTAAAGTGTTAGCTGTTTTCGATAAAAAACTTCTGAGTTGTGGAACCAACTCTCATTATCCTATCTGCATGTGGAGAAATATCGAAAATCTTCAGCAACTCGGAGGTTCTTCCACATATTTTGGCAAAGGATTCGTACCATATAATCCCCACTCAAAATCATCTTACACATTCTCAGATGACGGAAGATTTTTTTCTGGAGTAAAGATGGAGTTTGGAGGTCAAGACAACGCAATTACTGCAAATGAATTCGACAAATTCAAACTTTCTAGCCAACTTAGGACTCTTCGACATAACCATTACTGGCTGGATGATCCTGTTTTTCGTCGAAGTTTTCTAATTGGAGattacatttatttattcttcgACGAATTTGCACGCGAATGTTCAGATTGTGACGCGGTGCGGTACTCAAGAGTGGCTAGAATTTGCAAGGGCGACACTGGAGGGAATGACATGACGCTTTGGGTAAACTTCGTTACCTTTCAAAAAGCAAGATTAAATTGTTCCTTGCCTGGAGCATATCcatttcattttaatattttgcATGATATCCACTGGGATGCACGAACCACAACATTTTACGGGGTATTTACAACGGGACGAAGCCATAACTATTATACTTCAGCCATTTGTCCTTACTCCCTAATGGATGTTGACGAAGTCTTTACCGGAACGTTTAAACATAAAGAAGACGGTTTTTGGAAGGAGAAAACGAATCCAGGACATATAAACGAGTGCACAGTGAACACCAGGTCTCTGCTATATGCACCAGACCCATCAGAAATATTGCGGGGCAGAATGCCAACCAGGTCTATGACGTCCTCCTCGATTTACGAGCAGAGTCAGTGTATTTTGACGACTAAAGTGGTCCAACCAAGATCAATTGTGACTCCATTTTATCTTCACGATATCAGATTCATTAAAGTAGCGACGATATCTTTCCAAACCAATCAAAATGAGAGCAGAGAAGTTTGGTACATAGCAACAGATAGAGGAACCATTTTAAAACTATCAAGGACCCCAATAATTAAggaattttgtatttttgaggAATACGAGATATTTCAGAacaataaaaaagaacaaataaaagcAATGGAAATGTCACCAGATAAGGAAAGTCTTATCATTGGATCTGACACTAAGTTAATAAAACTGCCATTACTTCGTTGTGATAGATATGTCAACAAGAGATCCTGTTTAGAAGGCAAAGATCCACTTTGTGGCTGGAGTATGTCGGAAGGGAAGTGCAACCCCTGGACTAAACGGAGCAAAATAGATTGGGAACAAAATATTACGTCTTGCCCACAACGTGAAGCGAAATGGTCTGAGTGGTCATCTTGGAGCGAGTGCTTGAGAGATGATAAAAACTTATGTAAATGCCGGAGAAGAACGTGTGTGAATGCTCGCATGTTTTACAATTGTCACGGGGCTgacattgaattaaaaaattgcACAGTTGACGTATCGACATTAACCAATACGGAGGATTGGTGGAGGAACGGAGTAGTGAACGGTGGATGGTCTGAATGGTCAAAATGGTCAGACTGTCTCCGTGGGTATAGAAACAGATCACGAACATGCACAAAACCATTACCGAAAAATGGAGGATCTAACTGTAAAAATAGCAACAAGGAGTACACGATATGTGAACCTGTAAGATTTGATGATGCCAAGACATTTATGTGGACAAGTTGGAGTAGAGTCCGCGGTCCAGAGAAGAAGGCAATCAGATATAAAATATCTTGCAGTTCAAGAGCTGTCGTAATGAAGAACTTGCAAATAGATGTGCTTCGCAACGAAACTGTTCAATGTAACAAGAGTCTTTGCATTGATCCACCGACACGTCTACATCGTTTTCTGAACAACTGGGGTCCTTGGTTATCTTGCAAGGGTAACACGACAAAACTTCGTACACGTCAACTGTGCACTCAAAATCTTACAAGTCACTGGTCTTGCAACCAACATGATATCGAAAGAACTGTTGATCTTCAGAATGGAAGAAACAAATCTTCAGAAAAATCTACAGATACAAAGGTTCATCTTCCAACCACAGATCCTCTTGGCACTGACTGGTTCCGATGGTCTCCCTGTGTGTGTGAACACGATGTCACACTGACTAGTTCGTCACTTGGTATTCAACACAGAAAAATACCACAAGGAGATAAAACTGCTACTGAGTATAGAACATGCCCATGTGAAGTAATCCAGTTAAAGAGTACGAACAATCCAGGTTTGGTCGACGTAAGACAATCTCTTGGGGAGCCGTCTGATGATGGAGAGTACTCACTTACAATGGTCGTTATCATCGTGTGTACATGTTGTGCAGCTTGTGTTGTCGTCACTGCATTCCTGCTCATTATGTACCATCGTAGGAAAGAGCGaatagtaaaacaaaaaagcagTAACTGTAAGCACATATCAATCAGCCAAAGCGACCAACCAAATGGCACAGCGTTAtga

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9VTT0	Semaphorin 5c OS=Drosophila melanogaster OX=7227 GN=Sema5c PE=1 SV=3
Q8NFY4	Semaphorin-6D OS=Homo sapiens OX=9606 GN=SEMA6D PE=1 SV=1
Q5R7F5	Semaphorin-6D OS=Pongo abelii OX=9601 GN=SEMA6D PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001633 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00090 all species →	TSP_1	Thrombospondin type 1 domain	Domain	Interproscan
PF01403 all species →	Sema	Sema domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036383 all species →	Homologous_superfamily	Thrombospondin type-1 (TSP1) repeat superfamily	Interproscan
IPR027231 all species →	Family	Semaphorin	Interproscan
IPR001627 all species →	Domain	Sema domain	Interproscan
IPR036352 all species →	Homologous_superfamily	Sema domain superfamily	Interproscan
IPR000884 all species →	Repeat	Thrombospondin type-1 (TSP1) repeat	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11036 all species →	SEMAPHORIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0001755 all species →	Biological Process	neural crest cell migration	Interproscan
GO:0030215 all species →	Molecular Function	semaphorin receptor binding	Interproscan
GO:0030335 all species →	Biological Process	positive regulation of cell migration	Interproscan
GO:0045499 all species →	Molecular Function	chemorepellent activity	Interproscan
GO:0048843 all species →	Biological Process	negative regulation of axon extension involved in axon guidance	Interproscan
GO:0005515 all species →	Molecular Function	protein 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
K06841	SEMA5; semaphorin 5	-	Axon guidance	ko04360	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000016450.1 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

79.2Max TPM

41.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	50.36	79.18
polyp and skeleton · 31C, 3week	6	6	19.74	37.00
polyp and skeleton · 28C, 3week	6	6	32.73	48.56
polyp and skeleton · 26C, 3week	4	4	53.15	67.45
polyp and skeleton · 28C, 24hr	2	2	30.11	33.70
polyp and skeleton · 31C, 24hr	2	2	36.61	60.95

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
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	79.18
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	78.39
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	72.73
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	68.65
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	63.20
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	61.85
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	55.67
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	55.33
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	48.51
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	48.07
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	41.42
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	39.32
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	35.83
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	33.11
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	27.94
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	26.34
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	20.57
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	37.00
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	22.03
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	20.71
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	19.35
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	9.81
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	9.51
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	48.56
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	37.07
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	31.77
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	29.94
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	27.81
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	21.25
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	67.45
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	67.27
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	53.20
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	24.67
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	33.70
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	26.53
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	60.95
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	12.28

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	7	ENSBQFP00000010805	0.78828209606325
Negatively correlated	29	ENSBQFP00000010535	-0.734579357839714

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. Partner counts were matched on ENSBQFP00000016450, the spelling this network uses.

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 →