Gene detail

Detailed information of ENSBQFP00000001270.1 in Heliopora coerulea

Genomic Location: JASJOG010000008.1:612363...633042
NR annotation: CAB3979857.1, NAD(P) transhydrogenase, mitochondrial [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
Q02548	Paired box protein Pax-5 OS=Homo sapiens OX=9606 GN=PAX5 PE=1 SV=1
Q02650	Paired box protein Pax-5 OS=Mus musculus OX=10090 GN=Pax5 PE=1 SV=1
Q90268	Paired box protein Pax-2a OS=Danio rerio OX=7955 GN=pax2a PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000430 (this species only) · gene tree & orthology
Transcription factor family	Homeobox · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00292 all species →	PAX	'Paired box' domain	Domain	Interproscan
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001523 all species →	Domain	Paired domain	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR043182 all species →	Domain	Paired DNA-binding domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR043565 all species →	Family	PAX family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45636 all species →	PAIRED BOX PROTEIN PAX-6-RELATED-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0048856 all species →	Biological Process	anatomical structure development	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
K15608	PAX2; paired box protein 2	-	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000001270.1 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

36TPM > 0

6Conditions

260.8Max TPM

99.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	81.40	111.65
polyp and skeleton · 31C, 3week	6	6	125.49	157.41
polyp and skeleton · 28C, 3week	6	5	106.49	260.81
polyp and skeleton · 26C, 3week	4	4	108.37	191.33
polyp and skeleton · 28C, 24hr	2	2	95.54	103.16
polyp and skeleton · 31C, 24hr	2	2	146.64	163.52

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
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	111.65
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	108.71
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	96.97
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	93.07
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	91.72
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	90.54
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	88.47
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	87.05
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	85.04
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	81.19
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	74.83
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	73.27
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	65.03
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	63.25
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	59.34
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	58.77
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	54.84
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	157.41
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	144.08
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	132.26
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	125.74
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	123.48
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	69.99
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	260.81
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	103.92
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	97.01
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	91.84
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	85.39
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	0.00
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	191.33
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	83.64
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	80.75
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	77.79
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	103.16
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	87.92
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	163.52
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	129.75

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	18	ENSBQFP00000031753	0.916144055922044
Negatively correlated	37	ENSBQFP00000003592	-0.776994429635862

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 ENSBQFP00000001270, 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 →