Gene detail

Detailed information of OS493_019046-T1 in Lophelia pertusa

Genomic Location: scaffold_64:1701277...1712204
NR annotation: KAJ7372537.1, hypothetical protein OS493_019046 [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
F1QBY1	Nipped-B-like protein B OS=Danio rerio OX=7955 GN=nipblb PE=2 SV=1
Q6KCD5	Nipped-B-like protein OS=Mus musculus OX=10090 GN=Nipbl PE=1 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

Pfam accession	Pfam name	Description	Type	Source
PF12830 all species →	Nipped-B_C	Sister chromatid cohesion C-terminus	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR033031 all species →	Family	Scc2/Nipped-B family	Interproscan
IPR024986 all species →	Domain	Sister chromatid cohesion C-terminal domain	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_019046-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_019046-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

107TPM > 0

7Conditions

84.2Max TPM

5.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.09	5.85
polyp at pH7 6	18	16	3.31	7.76
coral polyp · control treatment	16	16	9.49	84.17
coral polyp · oil and dispersant treatment	16	16	7.06	55.18
coral polyp · oil treatment	16	16	4.24	7.32
coral polyp · dispersant treatment	16	16	4.00	7.52
Polyp	10	9	1.96	3.84

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.85
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.83
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.30
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.23
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.46
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.24
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.19
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.03
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.96
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.69
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.64
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.61
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.44
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.43
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.26
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.20
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.16
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.15
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.76
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.25
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.96
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.36
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.74
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.61
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.59
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.56
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.90
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.69
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.58
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.56
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.27
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.01
SRR11359500	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	84.17
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.73
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.92
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.89
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.61
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.29
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.11
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.59
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.35
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.24
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.03
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.77
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.22
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.98
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.92
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.07
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.18
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.91
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.70
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.58
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.53
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.17
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.57
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.41
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.29
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.97
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.90
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.58
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.21
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.92
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.32
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.09
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	6.76
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.86
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.06
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.55
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.21
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.03
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.64
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.28
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.15
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.46
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.43
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.52
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.91
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.52
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.48
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.98
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.80
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.62
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.63
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.54
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.48
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.45
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.18
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.16
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.49
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	3.84
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.14
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.96
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.52
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.07
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	2.07
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.35
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.91
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.75
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.