Gene detail

Detailed information of OS493_021306-T1 in Lophelia pertusa

Genomic Location: scaffold_81:704789...726390
NR annotation: KAJ7378724.1, Transcription elongation factor SPT6, partial [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
Q7KZ85	Transcription elongation factor SPT6 OS=Homo sapiens OX=9606 GN=SUPT6H PE=1 SV=2
Q62383	Transcription elongation factor SPT6 OS=Mus musculus OX=10090 GN=Supt6h PE=1 SV=2
Q8UVK2	Transcription elongation factor SPT6 OS=Danio rerio OX=7955 GN=supt6h PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003299 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14641 all species →	HTH_44	Helix-turn-helix DNA-binding domain of SPT6	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017072 all species →	Family	Transcription elongation factor Spt6	Interproscan
IPR023323 all species →	Homologous_superfamily	Tex-like domain superfamily	Interproscan
IPR023319 all species →	Homologous_superfamily	Tex-like protein, HTH domain superfamily	Interproscan
IPR028088 all species →	Domain	Helix-turn-helix DNA-binding domain of Spt6	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10145 all species →	TRANSCRIPTION ELONGATION FACTOR SPT6	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0008023 all species →	Cellular Component	transcription elongation factor complex	Interproscan
GO:0031491 all species →	Molecular Function	nucleosome binding	Interproscan
GO:0034728 all species →	Biological Process	nucleosome organization	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:0140673 all species →	Biological Process	transcription elongation-coupled chromatin remodeling	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14786	KRI1; protein KRI1	-	Ribosome biogenesis	ko03009	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_021306-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

110TPM > 0

7Conditions

29.8Max TPM

12.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	10.20	16.27
polyp at pH7 6	18	18	9.81	16.07
coral polyp · control treatment	16	16	16.17	25.92
coral polyp · oil and dispersant treatment	16	16	18.27	29.84
coral polyp · oil treatment	16	16	12.72	21.56
coral polyp · dispersant treatment	16	16	15.79	21.65
Polyp	10	10	4.49	7.25

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.27
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.47
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.81
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.08
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.80
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.61
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.56
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.22
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.96
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.94
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.63
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.17
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.14
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.52
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.04
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.01
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.63
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.07
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.02
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.87
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.32
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.97
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.27
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.49
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.21
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.16
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.99
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.78
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.36
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.13
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.54
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.83
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.47
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.81
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.27
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.92
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.41
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.07
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.73
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.45
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.52
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.07
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.97
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.21
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.93
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.18
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.92
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.79
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.17
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.12
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.34
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.84
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.81
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.55
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.48
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.39
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.30
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.14
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.66
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.50
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.26
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	17.10
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.34
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.13
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.18
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.54
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.17
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.56
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.45
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.36
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.26
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.22
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.39
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.16
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.77
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.27
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.89
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.05
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.89
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.58
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	8.03
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.36
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.22
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.65
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.34
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.32
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.44
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.95
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.89
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.89
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.71
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.54
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.53
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.45
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.99
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.41
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.37
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	7.25
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	6.12
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.28
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	5.14
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	4.58
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	4.05
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.82
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	3.26
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	2.26

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.