Gene detail

Detailed information of OS493_002878-T1 in Lophelia pertusa

Genomic Location: scaffold_6:1672752...1673963
NR annotation: KAJ7340151.1, Transcription factor Sox-8 [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
Q9BG91	Transcription factor SOX-9 OS=Callithrix jacchus OX=9483 GN=SOX9 PE=2 SV=1
P48436	Transcription factor SOX-9 OS=Homo sapiens OX=9606 GN=SOX9 PE=1 SV=1
P61753	Transcription factor SOX-9 OS=Macaca mulatta OX=9544 GN=SOX9 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006735 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan
PF12444 all species →	Sox_N	Sox developmental protein N terminal	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR022151 all species →	Domain	Sox developmental protein N-terminal	Interproscan
IPR050917 all species →	Family	SOX Transcription Factors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45803 all species →	SOX100B	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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
K18435	SOX9; transcription factor SOX9 (SOX group E)	-	Transcription factors	ko03000	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_002878-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

127.2Max TPM

31.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	28.12	49.54
polyp at pH7 6	18	18	33.73	58.08
coral polyp · control treatment	16	16	39.99	127.23
coral polyp · oil and dispersant treatment	16	16	23.26	72.10
coral polyp · oil treatment	16	16	33.48	76.05
coral polyp · dispersant treatment	16	16	37.39	77.18
Polyp	10	10	23.78	51.76

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.54
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.48
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.09
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.41
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.75
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.70
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.34
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.87
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.31
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.96
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.77
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.49
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.11
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.90
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.79
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.77
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.72
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.33
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.80
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.73
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.75
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.22
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.77
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.06
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.86
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.43
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.13
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.19
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.04
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.95
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.87
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.49
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	127.23
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.18
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.52
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.11
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.11
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.95
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.90
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.27
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.02
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.26
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.96
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.95
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.15
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.68
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.55
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	72.10
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.21
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.60
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.16
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.13
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.25
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.21
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.05
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	14.84
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.18
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.79
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.59
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.40
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	7.62
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.58
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.41
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.05
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	64.35
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.55
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.03
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.85
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.25
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.10
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.63
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.96
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.24
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.88
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.79
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.85
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.48
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	9.05
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	77.18
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	63.74
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.72
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	53.97
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	50.70
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.83
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.90
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.71
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.35
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.61
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.98
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.98
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.59
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.76
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.59
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	51.76
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	41.95
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	27.33
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	22.95
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	21.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	20.09
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	20.08
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.35
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	12.30
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	6.74

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.