Gene detail

Detailed information of OS493_002195-T1 in Lophelia pertusa

Genomic Location: scaffold_4:6541965...6575014
NR annotation: KAJ7375429.1, N-chimaerin [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
Q91V57	N-chimaerin OS=Mus musculus OX=10090 GN=Chn1 PE=1 SV=2
P15882	N-chimaerin OS=Homo sapiens OX=9606 GN=CHN1 PE=1 SV=3
P52757	Beta-chimaerin OS=Homo sapiens OX=9606 GN=CHN2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004109 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00017 all species →	SH2	SH2 domain	Domain	Interproscan
PF00130 all species →	C1_1	Phorbol esters/diacylglycerol binding domain (C1 domain)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000980 all species →	Domain	SH2 domain	Interproscan
IPR046349 all species →	Homologous_superfamily	C1-like domain superfamily	Interproscan
IPR002219 all species →	Domain	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Interproscan
IPR036860 all species →	Homologous_superfamily	SH2 domain superfamily	Interproscan
IPR051854 all species →	Family	Rho-type GTPase-activating protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46075 all species →	CHIMERIN FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0043087 all species →	Biological Process	regulation of GTPase activity	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_002195-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_002195-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

105TPM > 0

7Conditions

13.6Max TPM

5.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	5.50	9.96
polyp at pH7 6	18	15	5.73	11.40
coral polyp · control treatment	16	16	5.64	12.93
coral polyp · oil and dispersant treatment	16	16	5.84	13.55
coral polyp · oil treatment	16	16	3.74	10.05
coral polyp · dispersant treatment	16	15	4.58	8.77
Polyp	10	9	2.98	6.88

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.96
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.84
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.60
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.38
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.70
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.64
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.39
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.38
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.25
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.25
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.98
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.93
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.84
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.71
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.58
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.90
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.20
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.40
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.64
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.96
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.88
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.64
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.45
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.89
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	6.77
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.84
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.69
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.56
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.23
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.30
SRR11359513	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
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.93
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	11.70
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.15
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	9.82
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	7.44
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.14
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.34
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.33
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.60
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.23
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.01
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.58
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.31
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.29
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.72
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	13.55
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.27
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	11.19
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.46
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.76
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.64
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.53
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.29
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.06
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.12
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.95
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.90
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.80
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.09
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.01
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	10.05
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.61
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.52
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.23
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.98
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.81
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.06
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.05
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.68
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.63
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.94
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.79
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.67
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.77
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.68
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.27
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.17
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.68
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.66
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.58
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.27
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.86
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.72
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.58
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.44
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.22
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.44
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.03
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	6.88
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	5.52
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	3.99
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	3.80
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	3.71
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.69
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.13
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.68
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.