Gene detail

Detailed information of OS493_019049-T1 in Lophelia pertusa

Genomic Location: scaffold_64:1724911...1734343
NR annotation: KAJ7372540.1, hypothetical protein OS493_019049 [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
Q6KCD5	Nipped-B-like protein OS=Mus musculus OX=10090 GN=Nipbl PE=1 SV=1
F1QBY1	Nipped-B-like protein B OS=Danio rerio OX=7955 GN=nipblb PE=2 SV=1
Q6KC79	Nipped-B-like protein OS=Homo sapiens OX=9606 GN=NIPBL PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002809 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for OS493_019049-T1 in Lophelia pertusa.

InterPro

InterPro term	Type	Description	Source
IPR033031 all species →	Family	Scc2/Nipped-B family	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21704 all species →	NIPPED-B-LIKE PROTEIN DELANGIN SCC2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0034087 all species →	Biological Process	establishment of mitotic sister chromatid cohesion	Interproscan
GO:0061780 all species →	Biological Process	obsolete mitotic cohesin loading	Interproscan
GO:0071169 all species →	Biological Process	establishment of protein localization to chromatin	Interproscan
GO:0090694 all species →	Cellular Component	Scc2-Scc4 cohesin loading complex	Interproscan
GO:1990414 all species →	Biological Process	replication-born double-strand break repair via sister chromatid exchange	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_019049-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_019049-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

104TPM > 0

7Conditions

109.0Max TPM

4.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	17	2.43	3.91
polyp at pH7 6	18	15	2.22	3.98
coral polyp · control treatment	16	16	10.35	109.00
coral polyp · oil and dispersant treatment	16	16	7.62	71.93
coral polyp · oil treatment	16	16	3.45	5.50
coral polyp · dispersant treatment	16	16	4.15	7.11
Polyp	10	8	1.02	2.40

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	-	3.91
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.68
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.66
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.64
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.24
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.12
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.81
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.57
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.44
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.31
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.24
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.13
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.86
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.82
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.81
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.33
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.08
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.98
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.59
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.35
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.09
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.05
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.94
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.83
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.59
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.55
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.51
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.37
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.90
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.64
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.47
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	109.00
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.89
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.53
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.37
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.13
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.87
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.82
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.72
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.95
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.62
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.16
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.50
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.10
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.35
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.11
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.47
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.93
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.84
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.75
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.34
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.60
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.33
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.47
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.48
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.43
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.41
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.24
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.24
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.74
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.36
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.18
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.50
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.44
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.96
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.54
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.30
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.96
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.81
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.69
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.07
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.49
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.91
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.48
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.40
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.17
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.11
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.71
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.31
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.34
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.91
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.77
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.67
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.56
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.05
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.63
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.41
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.97
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.50
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.40
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.40
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	1.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.38
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	1.32
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.93
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.90
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.83
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.65
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.