Gene detail

Detailed information of OS493_016571-T1 in Lophelia pertusa

Genomic Location: scaffold_51:387712...396717
NR annotation: KAJ7379337.1, Lysine-specific demethylase 5A [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P29375	Lysine-specific demethylase 5A OS=Homo sapiens OX=9606 GN=KDM5A PE=1 SV=3
Q3UXZ9	Lysine-specific demethylase 5A OS=Mus musculus OX=10090 GN=Kdm5a PE=1 SV=2
Q5F3R2	Lysine-specific demethylase 5B OS=Gallus gallus OX=9031 GN=KDM5B PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004250 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02375 all species →	JmjN	jmjN domain	Family	Interproscan
PF01388 all species →	ARID	ARID/BRIGHT DNA binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003349 all species →	Domain	JmjN domain	Interproscan
IPR001606 all species →	Domain	ARID DNA-binding domain	Interproscan
IPR036431 all species →	Homologous_superfamily	ARID DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10694 all species →	LYSINE-SPECIFIC DEMETHYLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0032452 all species →	Molecular Function	histone demethylase activity	Interproscan
GO:0034647 all species →	Molecular Function	histone H3K4me/H3K4me2/H3K4me3 demethylase activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA 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 OS493_016571-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_016571-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples

107TPM > 0

7Conditions

109.5Max TPM

21.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	7.88	13.56
polyp at pH7 6	18	18	9.11	16.48
coral polyp · control treatment	16	16	26.18	76.30
coral polyp · oil and dispersant treatment	16	16	38.28	71.37
coral polyp · oil treatment	16	16	16.56	33.52
coral polyp · dispersant treatment	16	15	48.31	109.52
Polyp	10	8	2.63	5.82

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.56
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.68
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.64
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.56
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.23
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.99
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.85
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.55
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.47
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.25
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.15
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.97
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.96
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.14
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.76
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.28
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.30
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.48
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.34
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.24
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.62
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.92
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.99
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.63
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.12
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.06
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.89
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.88
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.67
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.35
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.36
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.26
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.20
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.48
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	76.30
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	67.50
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.17
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.93
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.54
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.15
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.53
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.11
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.97
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.36
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.52
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.00
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.44
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.59
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.37
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.20
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.69
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.43
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.66
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.59
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.34
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.95
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.45
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.21
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.86
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.96
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.98
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.32
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.25
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.15
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.52
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.68
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.78
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.06
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.51
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.85
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.37
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.54
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.95
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.68
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.51
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.86
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.59
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.28
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.34
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.51
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	109.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	100.56
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	85.03
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.80
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.50
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.59
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	47.43
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.23
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.18
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.64
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.92
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.55
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.75
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.78
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.82
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	4.12
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.45
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.35
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	2.94
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	1.56
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.50
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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.