Gene detail

Detailed information of OS493_015538-T1 in Lophelia pertusa

Genomic Location: scaffold_47:336486...337590
NR annotation: KAJ7360437.1, hypothetical protein OS493_015538 [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
Q91X96	Guanine nucleotide exchange factor MSS4 OS=Mus musculus OX=10090 GN=Rabif PE=1 SV=1
Q08326	Guanine nucleotide exchange factor MSS4 OS=Rattus norvegicus OX=10116 GN=Rabif PE=1 SV=1
P47224	Guanine nucleotide exchange factor MSS4 OS=Homo sapiens OX=9606 GN=RABIF PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007820 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04421 all species →	Mss4	Mss4 protein	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011057 all species →	Homologous_superfamily	Mss4-like superfamily	Interproscan
IPR007515 all species →	Family	Mss4	Interproscan
IPR011323 all species →	Homologous_superfamily	Mss4/translationally controlled tumour-associated TCTP	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13276 all species →	GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0007264 all species →	Biological Process	small GTPase-mediated signal transduction	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006892 all species →	Biological Process	post-Golgi vesicle-mediated transport	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0016020 all species →	Cellular Component	membrane	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
K19952	RABIF, MSS4, DSS4; guanine nucleotide exchange factor	-	Membrane trafficking	ko04131	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_015538-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

92.1Max TPM

32.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	22.86	36.70
polyp at pH7 6	18	18	24.66	37.36
coral polyp · control treatment	16	16	33.91	48.19
coral polyp · oil and dispersant treatment	16	16	45.66	92.06
coral polyp · oil treatment	16	16	37.75	63.97
coral polyp · dispersant treatment	16	16	35.76	67.02
Polyp	10	10	30.93	47.50

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.70
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.80
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	32.76
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.59
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.94
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.85
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.83
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.55
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	20.28
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.49
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.08
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.50
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.37
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.55
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.14
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.45
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.18
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.46
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.36
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.03
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.01
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.25
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.49
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	27.22
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.12
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.15
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.74
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.51
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.25
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	23.74
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.66
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.04
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.04
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.58
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.65
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.19
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.21
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.28
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.94
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.61
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.93
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.10
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	32.18
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.14
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.07
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	30.05
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.14
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.06
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.82
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.70
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.10
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.06
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.94
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	74.92
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.65
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.54
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.48
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.71
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.04
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	37.74
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.01
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	30.67
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.25
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.93
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.50
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.02
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.03
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.97
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.20
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.88
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.67
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.56
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.65
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.81
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.23
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.22
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.78
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	32.49
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.67
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.54
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.08
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	26.63
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.02
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	56.38
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	54.43
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.08
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.70
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.95
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.99
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	30.34
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	29.85
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.37
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.84
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	26.01
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.01
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.24
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.82
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	47.50
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	43.92
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	42.44
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	31.08
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	28.59
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	27.07
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	25.28
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	24.56
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	20.01
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	18.83

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.