Gene detail

Detailed information of OS493_022760-T1 in Lophelia pertusa

Genomic Location: scaffold_96:1015075...1023532
NR annotation: KAJ7330236.1, RAB3A interacting protein [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
Q8TBN0	Guanine nucleotide exchange factor for Rab-3A OS=Homo sapiens OX=9606 GN=RAB3IL1 PE=1 SV=1
Q2KJ58	Guanine nucleotide exchange factor for Rab-3A OS=Bos taurus OX=9913 GN=RAB3IL1 PE=2 SV=1
Q99NH3	Guanine nucleotide exchange factor for Rab-3A OS=Rattus norvegicus OX=10116 GN=Rab3il1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006037 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06428 all species →	Sec2p	GDP/GTP exchange factor Sec2p	Coiled-coil	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR040351 all species →	Family	Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2	Interproscan
IPR009449 all species →	Domain	GDP/GTP exchange factor Sec2, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14430 all species →	RABIN3-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0006887 all species →	Biological Process	exocytosis	Interproscan
GO:0070319 all species →	Cellular Component	Golgi to plasma membrane transport vesicle	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
K16779	RAB3IP, RABIN8; Rab-3A-interacting protein	-	Chromosome and associated proteins	ko03036	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_022760-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

115.2Max TPM

51.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	60.93	74.85
polyp at pH7 6	18	18	60.03	80.83
coral polyp · control treatment	16	16	56.42	115.21
coral polyp · oil and dispersant treatment	16	16	40.70	67.43
coral polyp · oil treatment	16	16	51.84	101.98
coral polyp · dispersant treatment	16	16	30.69	56.11
Polyp	10	10	60.31	111.55

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	-	74.85
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.29
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	64.10
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.54
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	63.14
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.94
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.28
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.48
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	61.34
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.99
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.56
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.33
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.02
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.65
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	51.89
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.74
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.81
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	80.83
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.42
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.01
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.48
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.02
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.91
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.63
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.57
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	62.17
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	61.77
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.87
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.88
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	55.71
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.16
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.59
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	48.87
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	39.78
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.81
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	115.21
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	101.22
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	70.08
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.22
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.64
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	53.77
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.35
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.29
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	46.19
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.24
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.17
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.19
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.35
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.65
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	67.43
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.02
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.66
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.36
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.28
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.85
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	36.36
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.75
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.92
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.27
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.08
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.45
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.84
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.14
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	101.98
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	82.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.81
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	66.51
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	65.43
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.18
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.44
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.48
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.42
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.38
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.36
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.66
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.50
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.27
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.39
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.11
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.41
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.59
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.57
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.45
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.81
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.92
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.62
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.24
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.86
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.98
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.63
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.08
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.83
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	16.50
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.45
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	111.55
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	72.51
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	70.01
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	57.76
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	55.03
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	53.48
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	51.33
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	50.55
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	45.44
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	35.46

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.