Gene detail

Detailed information of ENSBQFP00000006576.1 in Heliopora coerulea

Genomic Location: JASJOG010000012.1:1603826...1623543
NR annotation: CAB3978181.1, procollagen-lysine,2-oxoglutarate 5-dioxygenase 3-like [Paramuricea clavata]
Species Heliopora coerulea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSBQFT00000007219

ATGGTGCGTTTTCTTGTGACTTTTCTCGTAATCTTAGCTGGATTTTTCCCCGTACAGTTAGCAGAGGAGCACGACGCAACTCGAGGACTCAAGTTGGTGACTTTGACAGTAGCCACGGATGAGACTGATGGATTTAAAAGGTTCATGAGATCTGCCAACATTTTTGATATCCCCGTGAAGGTTGCTGGGATGCATGAAGAATGGAAGGGTGGAGACATGGAGCGTTACCCTGGTGGAGGACATAAATTAAACTTGTTACGAAGAGAAATTGAATGGTTGAAAAATGAGACCAACTTGGTAGTGATGTTCTCCGACAGCTATGATGTGATAATTACTGGTGGGCTAACAGAAATCCTGAAGAGATTCTTAGCTTTCAAAGCCAAAGTTGTGATTTCAGCTGAAGATTTTATATGGCCTGACAAGAGCCTAGAGAGTAAATACCCTCGTGTCAAGGAAGGAAAAAGATTTCTCTGTTCTGGAGGAATAATTGGTTATGCTCCACAAGTTTACAAACTGATGACAGCTCTTCCTATCAAGGACACAGATGATGATCAACTGTATTACACCAAGCTATACCTGGATGAAAACATCAAGAATGAACTTCAGATAAAGCTTGACCACAAGAGTGAAATTTTTCAGAATTTAAATGGAGCCACAGaggAAGTTCAAATAAAAACAGAAGATAGAGATATATGGTTAGAAAACACTAAATATGATACCAAACCTGTCGTAATCCATGGGAATGGTCCTTCTAAGttgtttttgaACTACATTACCAACTACATTCCCAAAGGATGGAATCTAATTGATGGCTGTGTAAGCTGTTCAGAAAACACATTCAGCATGAAAGATTATCAGccTGAAGACTACCCCAACGTTTTGGTGGCAATTTTTGTGGAAATTCCCACTCCCTTTTTCGCAGAATTCTTCAAACGATTGGTTGCACTTAATTATCCAAAAGATAAGATGGATATACTTATACATAACGTGGAACCGTTTCatgaaaaccaaatacaaacGTTTATCTCCTCCCATGGGAAATCCTATAAATCTGTCAATTATATCGCACCGAGGGATTACTTTAGTGAGACCAAGGCAAGGAATCATGCTGTTGAGTACTGCATTTCTAAGCAATGTAAGTATCTCTTTGTGCTGGACGCTGACGTGGTGATCACTGAACCAGAAACTCTAAAAATCCTGATAGAGCAAAACAGGTCCATCATTGCTCCTAAACTTTCCAAACATGGAAAGCTTTGGTCAAACTTCTGGGGAGATATAGGATACGACGGATTTTACTCACGTTCAAGGGATTATGTGGACATAGTAAACGGCAAGAGGAGAGGTGTGTGGAATGTACCGTACATATCCTCGGCTTATCTTGCTCACATCAGTGTCTTGGAACAACTAAAAAACCCATACAGCAGCAAGACTTTTGAAGCAGACATGGCTTTCTGTGCGTCATTAAGATCTAAGGGGATTTTTATGTACGTCGATAATTTAGTGCCTTTCGGCCGTTTGCTGGAGACCAGCAGGTTCACTACCACGAGGAAGCACAGTGACATGTACGAGATGATCACGAACCCACTGGATTGGGAagaaaaataccttcatccGGACTATTACAAAATCCGGACACCAGAGTGGAAAATGCAACAGCCATGCACCGATGTTTACTGGATACCACTTTTCTCGGAAACTTTTTCTACACACTTGTGGCAGGAATGCGAACACTTCGGGCAGTGGTCTGGTGGTGGACATGAGGATAAACGACTTGCTGGAGGCTACGAGAATGTCCCAACCGTCGACATTCACATGAACCAGATTGGATTTGAGCCTCAGTGGATGCATTATCTTAAGCATTACGTGGTGCCGATAGCCAACTACATATTCACTGGATATTATTCAGAGGCTCGTGCTATCATGAATTTCGTGGTGAAATATAACCCAGCAAAACAGTATTTTCTACGCCCTCATCATGATTCGTCAACATACACTATCAACGTTGCATTGAACAGAGCTGGAGTGGACTACGAGGGTGGCGGGGCACGATTTACGCGCTACAATTGTTCTGtgacaaatactaaaataggATGGGCACTGATGCATCCTGGTCGCCTGACCCATCAACACGAGGGATTGCCTACCACCAAAGGTACCCGCTACATCATGGTGTCTTTTATTGACCCATAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5U367	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 OS=Rattus norvegicus OX=10116 GN=Plod3 PE=1 SV=1
Q9R0E1	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 OS=Mus musculus OX=10090 GN=Plod3 PE=1 SV=1
Q5R6K5	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 OS=Pongo abelii OX=9601 GN=PLOD3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003861 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03171 all species →	2OG-FeII_Oxy	2OG-Fe(II) oxygenase superfamily	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029044 all species →	Homologous_superfamily	Nucleotide-diphospho-sugar transferases	Interproscan
IPR005123 all species →	Domain	Oxoglutarate/iron-dependent dioxygenase	Interproscan
IPR050757 all species →	Family	Collagen-modifying Glycosyltransferase 25	Interproscan
IPR044861 all species →	Domain	Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain	Interproscan
IPR006620 all species →	Domain	Prolyl 4-hydroxylase, alpha subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10730 all species →	PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE/GLYCOSYLTRANSFERASE 25 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0008475 all species →	Molecular Function	procollagen-lysine 5-dioxygenase activity	Interproscan
GO:0017185 all species →	Biological Process	peptidyl-lysine hydroxylation	Interproscan
GO:0005506 all species →	Molecular Function	iron ion binding	Interproscan
GO:0016705 all species →	Molecular Function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Interproscan
GO:0031418 all species →	Molecular Function	L-ascorbic acid 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

No KEGG orthology assignment for ENSBQFP00000006576.1.

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000006576.1 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

138.2Max TPM

59.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole coral	17	17	56.66	108.83
polyp and skeleton · 31C, 3week	6	6	57.14	86.30
polyp and skeleton · 28C, 3week	6	6	89.62	138.19
polyp and skeleton · 26C, 3week	4	4	57.02	77.00
polyp and skeleton · 28C, 24hr	2	2	45.74	56.10
polyp and skeleton · 31C, 24hr	2	2	25.58	30.43

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
ERR6178387	Whole coral	Whole coral	not recorded	not recorded	ERP120267	108.83
ERR6178782	Whole coral	Whole coral	not recorded	not recorded	ERP120267	72.77
ERR6178781	Whole coral	Whole coral	not recorded	not recorded	ERP120267	68.48
ERR6178388	Whole coral	Whole coral	not recorded	not recorded	ERP120267	67.25
ERR6178770	Whole coral	Whole coral	not recorded	not recorded	ERP120267	64.02
ERR6178389	Whole coral	Whole coral	not recorded	not recorded	ERP120267	63.71
ERR6178771	Whole coral	Whole coral	not recorded	not recorded	ERP120267	61.78
ERR6178775	Whole coral	Whole coral	not recorded	not recorded	ERP120267	58.40
ERR6178777	Whole coral	Whole coral	not recorded	not recorded	ERP120267	56.79
ERR6178780	Whole coral	Whole coral	not recorded	not recorded	ERP120267	55.61
ERR6178772	Whole coral	Whole coral	not recorded	not recorded	ERP120267	53.80
ERR6178776	Whole coral	Whole coral	not recorded	not recorded	ERP120267	44.73
ERR6178778	Whole coral	Whole coral	not recorded	not recorded	ERP120267	44.72
ERR6178783	Whole coral	Whole coral	not recorded	not recorded	ERP120267	43.25
ERR6178779	Whole coral	Whole coral	not recorded	not recorded	ERP120267	35.24
ERR6178773	Whole coral	Whole coral	not recorded	not recorded	ERP120267	33.45
ERR6178774	Whole coral	Whole coral	not recorded	not recorded	ERP120267	30.33
SRR12578065	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	86.30
SRR12587800	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	75.95
SRR12587804	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	72.82
SRR12587799	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	52.28
SRR12578066	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	34.35
SRR12578068	polyp and skeleton · 31C, 3week	polyp and skeleton	not recorded	31C, 3week	SRP115860	21.17
SRR12587802	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	138.19
SRR12587807	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	112.39
SRR12578067	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	92.45
SRR12587808	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	77.98
SRR5949849	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	70.47
SRR12587803	polyp and skeleton · 28C, 3week	polyp and skeleton	not recorded	28C, 3week	SRP115860	46.21
SRR12587806	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	77.00
SRR12587798	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	69.17
SRR12587805	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	64.76
SRR12587801	polyp and skeleton · 26C, 3week	polyp and skeleton	not recorded	26C, 3week	SRP115860	17.15
SRR12578063	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	56.10
SRR5949850	polyp and skeleton · 28C, 24hr	polyp and skeleton	not recorded	28C, 24hr	SRP115860	35.38
SRR12578064	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	30.43
SRR5949848	polyp and skeleton · 31C, 24hr	polyp and skeleton	not recorded	31C, 24hr	SRP115860	20.73

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	4	ENSBQFP00000033739	0.751151688672853
Negatively correlated	29	ENSBQFP00000051200	-0.489536046381735

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 ENSBQFP00000006576, 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 →