Gene detail

Detailed information of OS493_002582-T1 in Lophelia pertusa

Genomic Location: scaffold_5:4823970...4836757
NR annotation: KAJ7365860.1, LIM and senescent cell antigen-like-containing domain protein 2 [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
Q99JW4	LIM and senescent cell antigen-like-containing domain protein 1 OS=Mus musculus OX=10090 GN=Lims1 PE=1 SV=3
P48059	LIM and senescent cell antigen-like-containing domain protein 1 OS=Homo sapiens OX=9606 GN=LIMS1 PE=1 SV=4
Q2KJ33	LIM and senescent cell antigen-like-containing domain protein 2 OS=Bos taurus OX=9913 GN=LIMS2 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006852 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00412 all species →	LIM	LIM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001781 all species →	Domain	Zinc finger, LIM-type	Interproscan
IPR047946 all species →	Family	LIM and senescent cell antigen-like-containing domain protein 1/2-like	Interproscan
IPR047944 all species →	Domain	LIMS1/2-like, LIM domain 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24210 all species →	LIM DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005925 all species →	Cellular Component	focal adhesion	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005911 all species →	Cellular Component	cell-cell junction	Interproscan
GO:0045216 all species →	Biological Process	cell-cell junction organization	Interproscan
GO:0098609 all species →	Biological Process	cell-cell adhesion	Interproscan
GO:1900026 all species →	Biological Process	positive regulation of substrate adhesion-dependent cell spreading	Interproscan
GO:2001046 all species →	Biological Process	positive regulation of integrin-mediated signaling pathway	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
K23354	LIMS1_2, PINCH1_2; LIM and senescent cell antigen-like-containing domain protein 1/2	-	Domain-containing proteins not elsewhere classified	ko04990	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_002582-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

82.5Max TPM

32.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	40.84	54.58
polyp at pH7 6	18	18	40.11	54.86
coral polyp · control treatment	16	16	33.11	82.50
coral polyp · oil and dispersant treatment	16	16	24.08	67.77
coral polyp · oil treatment	16	16	28.11	54.60
coral polyp · dispersant treatment	16	16	20.21	29.93
Polyp	10	10	41.22	55.89

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	54.58
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.44
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	53.41
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.64
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.53
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	42.30
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.86
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	39.17
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.80
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.60
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.60
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.24
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.84
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.20
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.02
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.02
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.45
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.49
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.86
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.93
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.88
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.08
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.94
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.36
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.28
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.09
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.46
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.95
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.87
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.48
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.95
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.34
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.99
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.34
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.33
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.50
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.69
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.94
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.40
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.59
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.18
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.01
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.72
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.80
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.34
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.15
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.44
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.15
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.33
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.85
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.73
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.77
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.45
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.69
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.36
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.66
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.15
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	24.67
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.45
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.06
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.60
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	18.06
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.59
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.82
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.72
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.60
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.85
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.40
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.19
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.51
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	29.30
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.54
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.57
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.94
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	24.68
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.21
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.22
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.99
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.39
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.35
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.98
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.93
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.41
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.18
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.16
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.43
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.57
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.35
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.82
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.74
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.26
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.15
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.66
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.35
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.27
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.81
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	55.89
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	55.65
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	45.15
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	43.28
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	42.49
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	42.09
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	41.41
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	35.40
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	27.79
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	23.10

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.