Gene detail

Detailed information of OS493_028589-T1 in Lophelia pertusa

Genomic Location: scaffold_166:448339...450927
NR annotation: KAJ7370974.1, Protein SPT2 [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
Q6DGN6	Protein SPT2 homolog OS=Danio rerio OX=7955 GN=spty2d1 PE=2 SV=2
Q8IMP6	Protein SPT2 homolog OS=Drosophila melanogaster OX=7227 GN=CG5815 PE=2 SV=1
Q6NU13	Protein SPT2 homolog OS=Xenopus laevis OX=8355 GN=spty2d1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008432 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08243 all species →	SPT2	SPT2 chromatin protein	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013256 all species →	Family	Chromatin SPT2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22691 all species →	YEAST SPT2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0006334 all species →	Biological Process	nucleosome assembly	Interproscan
GO:0006360 all species →	Biological Process	transcription by RNA polymerase I	Interproscan
GO:0042393 all species →	Molecular Function	histone 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_028589-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_028589-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

105TPM > 0

7Conditions

27.8Max TPM

4.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	16	2.50	4.93
polyp at pH7 6	18	15	2.73	7.36
coral polyp · control treatment	16	16	6.23	9.69
coral polyp · oil and dispersant treatment	16	16	6.64	27.82
coral polyp · oil treatment	16	16	6.08	11.36
coral polyp · dispersant treatment	16	16	3.48	9.36
Polyp	10	10	3.46	13.66

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.93
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.47
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.24
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.86
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.58
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.53
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.42
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.37
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.22
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.15
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.12
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.05
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.52
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.36
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.30
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.99
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.92
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.83
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.21
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.66
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.60
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.30
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.22
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.81
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.47
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.61
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.69
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.62
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.89
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.51
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.19
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.90
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.68
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.49
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.42
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.87
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.44
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.15
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.40
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.90
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.82
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.22
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.25
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.92
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.71
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.77
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.64
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.11
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.97
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.95
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.81
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.66
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.66
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.60
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.47
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.67
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.36
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.10
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.19
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.68
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.63
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.43
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.02
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.88
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.78
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.98
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.26
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.75
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.66
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.77
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.30
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.56
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.36
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.28
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.05
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.69
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.31
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.15
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.29
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.18
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.73
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.57
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.02
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.96
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.91
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.01
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.02
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	13.66
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	3.96
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.44
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.00
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.88
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.27
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	2.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	1.22
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.04
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.03

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.