Gene detail

Detailed information of OS493_022917-T1 in Lophelia pertusa

Genomic Location: scaffold_98:985029...986045
NR annotation: KAJ7384283.1, hypothetical protein OS493_022917 [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
Q5FWM3	Transcription factor Sox-3-B OS=Xenopus laevis OX=8355 GN=sox3-b PE=2 SV=1
Q6EJB7	Transcription factor Sox-3 OS=Danio rerio OX=7955 GN=sox3 PE=1 SV=1
Q68FA4	Transcription factor Sox-3 OS=Xenopus tropicalis OX=8364 GN=sox3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000488 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00505 all species →	HMG_box	HMG (high mobility group) box	Domain	Interproscan
PF12336 all species →	SOXp	SOX transcription factor	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050140 all species →	Family	SRY-related HMG-box transcription factors	Interproscan
IPR036910 all species →	Homologous_superfamily	High mobility group box domain superfamily	Interproscan
IPR009071 all species →	Domain	High mobility group box domain	Interproscan
IPR022097 all species →	Family	Transcription factor SOX	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10270 all species →	SOX TRANSCRIPTION FACTOR	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:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0009653 all species →	Biological Process	anatomical structure morphogenesis	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	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_022917-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_022917-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

156.8Max TPM

70.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	92.93	149.45
polyp at pH7 6	18	18	82.30	113.64
coral polyp · control treatment	16	16	76.24	116.97
coral polyp · oil and dispersant treatment	16	16	37.73	74.61
coral polyp · oil treatment	16	16	81.54	156.83
coral polyp · dispersant treatment	16	16	49.27	123.18
Polyp	10	10	65.98	108.68

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	149.45
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	148.26
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	132.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	125.39
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	100.70
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	98.06
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	97.74
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	97.50
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	93.62
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	89.17
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.80
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	87.23
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.88
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	68.40
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.00
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	58.65
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.26
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.04
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.64
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	106.06
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	101.22
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	100.23
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	92.70
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	91.55
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	90.78
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	89.77
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.69
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.44
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	77.93
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.04
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.95
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.99
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.53
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.36
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.33
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.15
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	116.97
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.25
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	99.63
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.55
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.33
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	89.94
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	73.18
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.99
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.16
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.58
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.87
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.92
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.54
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.81
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.70
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	49.42
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.61
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.84
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.20
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.20
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.06
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	43.72
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.10
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.86
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.17
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.22
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.40
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	20.65
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.06
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.20
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	156.83
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	119.92
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.77
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	106.82
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	101.15
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	99.89
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	90.36
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.18
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.56
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.19
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.44
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.38
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.61
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.98
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.83
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	123.18
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	109.00
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.18
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.08
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.17
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.63
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	48.10
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.97
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.84
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.61
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.55
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.49
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.61
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.11
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.22
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.51
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	108.68
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	93.84
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	91.69
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	89.69
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	84.31
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	83.57
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	40.96
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	30.40
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	19.09
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	17.57

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.