Gene detail

Detailed information of ENSBQFP00000051443.1 in Heliopora coerulea

Genomic Location: JASJOG010000612.1:48970...76994
NR annotation: XP_028396442.1, lysine-specific demethylase 2B-like [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSBQFT00000058483

ATGGAGGTGGAAAGTGGTCGAAACCTGGTGGGTATTTTATCGTTTTACATCGGGAATTCGAGATACAACGTTGGATATTATTCTGGCACGTTGAACGGAATATTTCGACAACAGTATGTTTATTTCGTTTGCATTTTGTATACGTTTCAGAGAGCCTGTACACGGAAGAATTACGAGGACAACCTTGACGATGAGATTGAAGGCAAACGAACGTTCAGCGTTATGGAGAAGCTTCGggatgaaaaatttcaccagaatGACCGGTTCAAATTTACCACCGTACTAGCGAATGCTAATGATTTACTTCATTTTCCAGCCATAAACCTAAAATACATTCAAGAGCACGGCTTCGACTCACCGTTCCTGTTCAAGGCCAGCGAAGGATTAGGAATGAGAATGCCGTCTTCGGACTTCACTGTTGAAGATGTCAAACAACTCGTTGGTTCTAGGCGAGTTATAGACGTTATTGATGTGAACACCCAGCAACAGATTGAGATGTCTATGATGCAGTTTGCTCGCTATTACGCCAATCCTAATCGAGACAAAATTTACAACGTAATCAGCCTGGAATTCAGCCATACTAAACTGGAGAATTACATACAAACACCACTGTTGGTGCGTCAGCTGGATTGGGTGGACAATGTTTGGCCCAAAGAACTCATTCGTCAACAGACAGACTCGACGAATAATATGGATGACATGAAGTATCCTAAAGTTAGAAAATATGTTTTGATGAGTGTCCGCGATAGTTACACGGATTTTCACATCGATTTCTGTGGTTCCTCGGTTTGGTATCATGTTATCAGGGGGAAGAAGATTTTCTGGCTCATTCCGCCGACTGAAGAGAACCTCGCCATCTACGAGCAATGGGTGCTTTCAGGCAAACAACAGGATGTGTTTCTGGGCGATAAGGTCGAGAAATGCGCCATAGTGGAATTAGAGGCGGGAAACACTTTTCTTATGCCTTCAGGTTGGATCCATGCTGTGTACACGGCGGAGGACAGCTTGGTGTTCGGTGGAAACTTCATCCATAGCTACAACATAGAGCGACAATTCAAGATATGTGACATTGAGGAGCGTACCAGGGTTCCCAAGAAGTTCCGTTATCCCCTGTATACGCAGATCATGTGGTACTTGATGGAGGGGTATACTGCTTTACTCGAGCGAGACCGAGAGGAGCGGAACAAGTTGAATGAATTCCAAGAACCAGTCAAGGTGAAGGTTGAGGAAAAAGAAATGGTAATGGAGGAAGAAAATGGTAACAAGGAGAAAGAGAAGCCCGAAGAGGGATCTAAAAGCACTCCTAAAAAACTCTGGAACCCAGTGTACCTGGCGTCCCGAGAGGTGGAGGGGCTGCTTATGGTAATCGACAGAATGAGAAAGTGGCCAAAGACCAATATTCCTGATACGATTCAAAAGCCCGACGAACTTCTCGATCGTTTACAGGTAATTTTGTTCTTATCGTGTAACGCAGTATATGTTTACGATTTACGTCTTGTGCCGTCATCTTTATCTTATTCTTCACCCGTCCACAATAGATCATGTTTCCGTCTGTTGACTTCATTTGTCCTTTCATTTCCAGGAGCTATTACAGTCACAAAGAAACAACGACCCTACCTTAGCCTCGACGGGCCAACAGTACTTAAATCTAAGAAACCCAAGAGCATTCGAGCAAAGGTAAGGAAGCCTGGTACGAGTCTTCGTCGTCGTCGCACGAGGTGTCGTGCCTGCGAATCGTGTCTGCGTGAGGACTGTGGCGAGTGCAAGATGTGCAAAGACATGAAGAAGTTTGGAGGACCTGGGAGAATGAAGCAAACTTGCTTAATGCGCCAGTGTGAAAACCCAACGTTGCCAGTTTGTGCAACATGCGATGCTTGTGAGACACGTCACTCGGACGACGAAAATACGTTGATGGAATGCGTGGAGTGCGCGGCCATCGTACATCCCACGTGCCTGAGTCCCGGAGGTTTTTACTCCATCGTACCAGATGTCAACAACTGCTGGAAGTGCCCGAAATGTTGCGACGAGGCGACGGTAAGACTAACACTTTTCGCAGACCTTAAACAATCGCAAATAAAATCTCTTTCGCAAAAGAAAtggcttccgcttaggtctcttggtagctcaatggttagatcgtctcaccagtcatcagaaggttccggcatcgatcccagtctggggctcagaaatcgtttttctgaggatagaGAAGAGAATGAGGACAGCAACGACGAAGATAGCGCGCCGCTTTCTTCTCTGGCTAAAAAGACCAGAAAAGCGACTCCTCCGCCACCCACAGAAATACCTTTTGTCCCGCCACAGGAAGTCACACCCACGTATGTGGTACGTCCTCGCCCCATAACTCCTCCACCAGATACCCTTGTGCTGGAAAGCGAGACTGTTCACGTGATGAAGCGCGAATGCTGGCTCAAGATTTTTGAGTACCTCTCGCAGGCTGAGCTGTGTAAATGTATGCGCGTGTCACGCACGTGGAACCGATGGTGCATGGATAAAAAATTCTGGACGAAAATCAAGCTTCCCATTGGTCGACCGATTACAGCCTCGGCGCTGTTTGGCGTCGTTCGTCGACAGCCACTTCATCTCGACCTGAGCAACACGAATATTACCCAGCAACAATTGGCGTGGTTTCTCAGCCGTTTGCCAAGGCTCCGTGAACTGCTACTCGGCGCGTCGACTTTTGCAACAGTTGGCGCATTCACCCGTGTGACATGCCCGCCTATCAAGGTCCTGGACCTGAGTTGGTCTGAAAAAATCACCGACCGCGTGATCGAAGATTTGTTAAAACCTTCCAACAACGGAAGGCGGGAACGCGTCCCAGGTCCTGGGGAGAACGCCAGTCGATTACGATTCCTAACTGACTTGCGACTATCTGGCTGTGACGTCACCGATGCGAGTCTGCGGTACATCAAGCGGTTTCTGTATTGCCTTTCTCGGTTAGACCTGAGCTACTGCGTAATGATAACAGACGAAGGCGTAGCCGCTTTAATGGAGTCAGATTCTTCGTTTCACAAGAACATCAGAGAGCTGAACTTGACTGGGTGTACTAATGTGACAGATGCGTGCTTAGAAGCTCTGAAGAGGGCTCAGAACCTCGCCAAGATTGATTTGAGAAAGTGCGATCGAGTTCACGCTAAAGCTTTCAAAGAGTTTGTAAAATTCCGTGGAGCTGCTTCAATAGTTTTGAGATCATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9Y2K7	Lysine-specific demethylase 2A OS=Homo sapiens OX=9606 GN=KDM2A PE=1 SV=3
P59997	Lysine-specific demethylase 2A OS=Mus musculus OX=10090 GN=Kdm2a PE=1 SV=2
Q5U263	Lysine-specific demethylase 2A OS=Xenopus tropicalis OX=8364 GN=kdm2a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001395 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|PHD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16866 all species →	PHD_4	PHD-finger	Domain	Interproscan
PF13516 all species →	LRR_6	Leucine Rich repeat	Repeat	Interproscan
PF13621 all species →	Cupin_8	Cupin-like domain	Domain	Interproscan
PF17811 all species →	JHD	Jumonji helical domain	Domain	Interproscan
PF12937 all species →	F-box-like	F-box-like	Domain	Interproscan
PF02008 all species →	zf-CXXC	CXXC zinc finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001810 all species →	Domain	F-box domain	Interproscan
IPR019787 all species →	Domain	Zinc finger, PHD-finger	Interproscan
IPR002857 all species →	Domain	Zinc finger, CXXC-type	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR003347 all species →	Domain	JmjC domain	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan
IPR050690 all species →	Family	JHDM1 Histone Demethylase	Interproscan
IPR041667 all species →	Domain	Cupin-like domain 8	Interproscan
IPR006553 all species →	Repeat	Leucine-rich repeat, cysteine-containing subtype	Interproscan
IPR041070 all species →	Domain	Jumonji, helical domain	Interproscan
IPR001965 all species →	Domain	Zinc finger, PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23123 all species →	PHD/F-BOX CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003712 all species →	Molecular Function	transcription coregulator activity	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0006482 all species →	Biological Process	protein demethylation	Interproscan
GO:0032452 all species →	Molecular Function	histone demethylase activity	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
K10276	FBXL10_11, KDM2; F-box and leucine-rich repeat protein 10/11	EC:1.14.11.27	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 ENSBQFP00000051443.1 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

35TPM > 0

6Conditions

203.5Max TPM

88.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	16	57.38	99.81
polyp and skeleton · 31C, 3week	6	6	124.45	166.38
polyp and skeleton · 28C, 3week	6	5	97.21	168.90
polyp and skeleton · 26C, 3week	4	4	118.97	203.53
polyp and skeleton · 28C, 24hr	2	2	115.24	122.94
polyp and skeleton · 31C, 24hr	2	2	136.27	157.43

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
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	99.81
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	91.42
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	79.17
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	77.17
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	72.43
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	66.41
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	65.41
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	61.81
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	59.24
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	52.93
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	50.21
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	43.53
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	43.19
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	42.24
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	39.30
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	31.25
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	0.00
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	166.38
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	155.99
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	143.81
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	112.91
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	89.42
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	78.18
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	168.90
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	118.03
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	112.97
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	103.52
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	79.86
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	203.53
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	118.56
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	77.94
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	75.86
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	122.94
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	107.55
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	157.43
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	115.11

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	ENSBQFP00000026155	0.861041926875442
Negatively correlated	80	ENSBQFP00000003592	-0.884334060169986

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 ENSBQFP00000051443, 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 →