Gene detail

Detailed information of ENSBQFP00000035962 in Heliopora coerulea

Genomic Location: JASJOG010000152.1:651196...660272
NR annotation: CAB4023907.1, cell cycle checkpoint control RAD9A-like [Paramuricea clavata]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9Z0F6	Cell cycle checkpoint control protein RAD9A OS=Mus musculus OX=10090 GN=Rad9a PE=1 SV=1
Q99638	Cell cycle checkpoint control protein RAD9A OS=Homo sapiens OX=9606 GN=RAD9A PE=1 SV=1
Q6WBX8	Cell cycle checkpoint control protein RAD9B OS=Homo sapiens OX=9606 GN=RAD9B PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004776 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04139 all species →	Rad9	Rad9	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR026584 all species →	Family	Rad9	Interproscan
IPR007268 all species →	Family	Rad9/Ddc1	Interproscan
IPR046938 all species →	Homologous_superfamily	DNA clamp superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15237 all species →	DNA REPAIR PROTEIN RAD9	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000077 all species →	Biological Process	DNA damage checkpoint signaling	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0030896 all species →	Cellular Component	checkpoint clamp complex	Interproscan
GO:0000076 all species →	Biological Process	DNA replication checkpoint signaling	Interproscan
GO:0031573 all species →	Biological Process	mitotic intra-S DNA damage checkpoint signaling	Interproscan
GO:0071479 all species →	Biological Process	cellular response to ionizing radiation	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
K10995	RAD9B; cell cycle checkpoint control protein RAD9B	-	DNA repair and recombination proteins	ko03400	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000035962 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

30TPM > 0

6Conditions

82.6Max TPM

17.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	14	14.25	23.20
polyp and skeleton · 31C, 3week	6	6	17.46	33.82
polyp and skeleton · 28C, 3week	6	4	14.06	24.79
polyp and skeleton · 26C, 3week	4	2	15.14	31.37
polyp and skeleton · 28C, 24hr	2	2	23.96	27.66
polyp and skeleton · 31C, 24hr	2	2	47.19	82.65

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
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	23.20
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	22.79
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	20.69
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	20.53
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	18.18
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	17.77
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	17.06
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	16.91
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	16.20
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	14.45
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	14.18
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	14.01
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	13.70
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	12.56
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	0.00
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	0.00
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	0.00
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	33.82
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	20.85
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	18.15
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	13.61
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	11.94
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	6.37
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	24.79
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	24.06
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	21.98
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	13.51
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	0.00
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	0.00
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	31.37
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	29.21
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	0.00
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	0.00
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	27.66
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	20.27
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	82.65
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	11.74

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	31	ENSBQFP00000003016	0.919756151161744
Negatively correlated	12	ENSBQFP00000029230	-0.771709448658248

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 →