Gene detail

Detailed information of OS493_036463-T1 in Lophelia pertusa

Genomic Location: scaffold_365:262505...263069
NR annotation: KAJ7351128.1, SLIT-ROBO Rho GTPase-activating protein 3 [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
B0S6J3	SLIT-ROBO Rho GTPase-activating protein 2 OS=Danio rerio OX=7955 GN=srgap2 PE=2 SV=1
P98171	Rho GTPase-activating protein 4 OS=Homo sapiens OX=9606 GN=ARHGAP4 PE=1 SV=2
P29355	Sex muscle abnormal protein 5 OS=Caenorhabditis elegans OX=6239 GN=sem-5 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004563 (this species only)
Ubiquitin family	UBD\|Other\|SH3 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00018 all species →	SH3_1	SH3 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan
IPR001452 all species →	Domain	SH3 domain	Interproscan
IPR051627 all species →	Family	SLIT-ROBO Rho GTPase-activating	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14166 all species →	SLIT-ROBO RHO GTPASE ACTIVATING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030336 all species →	Biological Process	negative regulation of cell migration	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_036463-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_036463-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

79.5Max TPM

34.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.77	38.55
polyp at pH7 6	18	18	23.86	37.06
coral polyp · control treatment	16	16	49.50	79.46
coral polyp · oil and dispersant treatment	16	16	50.07	67.51
coral polyp · oil treatment	16	16	39.76	62.17
coral polyp · dispersant treatment	16	16	33.18	55.62
Polyp	10	10	9.97	15.50

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.55
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.22
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.93
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.47
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.88
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	29.86
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.67
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.60
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.73
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.47
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.80
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.60
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.31
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.86
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.35
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.18
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.89
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.06
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.46
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.19
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.72
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.94
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.59
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.20
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.84
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.11
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.49
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.72
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.12
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.48
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.82
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.11
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	11.31
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.97
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.46
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	69.55
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.47
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.23
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.65
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	55.47
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	54.75
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.89
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.50
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.14
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.16
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.36
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.32
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.75
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.27
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	15.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.51
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	64.55
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	63.17
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.05
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.51
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	56.20
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	55.64
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.63
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.61
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.55
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	46.89
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.16
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.05
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.96
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.93
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.72
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	62.17
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	52.41
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	51.56
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.28
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.05
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	47.23
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.80
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.98
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.70
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.36
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.64
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.98
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.13
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.19
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	55.62
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.17
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.65
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	41.33
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	39.62
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	38.09
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.77
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.67
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.58
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.32
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.83
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.82
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.28
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.26
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.14
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	15.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	15.14
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	11.87
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	11.14
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	10.70
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	9.85
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	8.87
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	7.26
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	6.23
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	3.15

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.