Gene detail

Detailed information of OS493_007852-T1 in Lophelia pertusa

Genomic Location: scaffold_17:3749666...3754249
NR annotation: KAJ7365201.1, hypothetical protein OS493_007852 [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
Q6PDG5	SWI/SNF complex subunit SMARCC2 OS=Mus musculus OX=10090 GN=Smarcc2 PE=1 SV=2
Q8TAQ2	SWI/SNF complex subunit SMARCC2 OS=Homo sapiens OX=9606 GN=SMARCC2 PE=1 SV=1
Q92922	SWI/SNF complex subunit SMARCC1 OS=Homo sapiens OX=9606 GN=SMARCC1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004403 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16495 all species →	SWIRM-assoc_1	SWIRM-associated region 1	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR032451 all species →	Domain	SMARCC, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12802 all species →	SWI/SNF COMPLEX-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0016514 all species →	Cellular Component	SWI/SNF complex	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:0045893 all species →	Biological Process	positive regulation of DNA-templated transcription	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_007852-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_007852-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

102.8Max TPM

38.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	36.86	64.22
polyp at pH7 6	18	18	38.17	69.23
coral polyp · control treatment	16	16	41.95	63.60
coral polyp · oil and dispersant treatment	16	16	33.84	78.94
coral polyp · oil treatment	16	16	41.14	80.59
coral polyp · dispersant treatment	16	16	32.63	61.04
Polyp	10	10	53.13	102.76

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.22
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.72
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.43
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	45.79
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.03
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.36
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.62
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.22
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.15
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.08
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.74
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.41
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.11
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.85
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.43
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.09
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.44
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.23
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	63.86
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.99
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	47.75
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	46.45
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.68
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.26
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.27
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.61
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.58
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.56
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.20
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.42
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.42
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.14
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.97
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	63.60
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.49
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.06
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.52
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.47
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.29
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.47
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	41.32
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.65
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.75
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.76
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.76
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.55
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.27
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	78.94
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.98
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.62
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.82
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.71
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.17
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.67
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.40
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.46
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.16
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.76
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.89
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.34
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.22
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	15.58
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.59
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.32
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.76
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.46
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.11
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.67
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.98
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.69
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.22
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.57
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.51
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.95
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.70
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.70
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.00
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	61.04
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	51.78
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	49.65
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.10
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.01
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.52
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.00
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.19
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.49
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.08
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.83
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.03
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.88
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.66
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.08
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.67
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	102.76
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	73.63
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	65.92
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	57.53
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	56.82
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	53.20
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	46.46
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	33.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	27.65
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	14.38

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.