Gene detail

Detailed information of OS493_028745-T1 in Lophelia pertusa

Genomic Location: scaffold_168:476936...479330
NR annotation: KAJ7326022.1, Trafficking protein particle complex subunit 4 [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
Q2TBL9	Trafficking protein particle complex subunit 4 OS=Bos taurus OX=9913 GN=TRAPPC4 PE=2 SV=1
Q9ES56	Trafficking protein particle complex subunit 4 OS=Mus musculus OX=10090 GN=Trappc4 PE=1 SV=1
Q69BT7	Trafficking protein particle complex subunit 4 OS=Rattus norvegicus OX=10116 GN=Trappc4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008307 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04099 all species →	Sybindin	Sybindin-like family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007233 all species →	Family	Trafficking protein particle complex subunit	Interproscan
IPR011012 all species →	Homologous_superfamily	Longin-like domain superfamily	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23249 all species →	TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030008 all species →	Cellular Component	TRAPP complex	Interproscan
GO:0006888 all species →	Biological Process	endoplasmic reticulum to Golgi vesicle-mediated transport	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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_028745-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_028745-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

109TPM > 0

7Conditions

45.9Max TPM

18.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	12.67	19.32
polyp at pH7 6	18	17	15.03	25.25
coral polyp · control treatment	16	16	22.03	31.27
coral polyp · oil and dispersant treatment	16	16	29.05	45.91
coral polyp · oil treatment	16	16	20.58	31.48
coral polyp · dispersant treatment	16	16	13.92	21.02
Polyp	10	10	17.71	30.50

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.32
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.29
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	18.35
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.20
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.97
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.69
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.17
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.94
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.72
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.48
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.41
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.23
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.65
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	9.41
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	8.01
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.93
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	7.32
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	25.25
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.85
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	19.75
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.39
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.29
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.54
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.28
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.94
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.55
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.08
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.99
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.45
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.97
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	12.26
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.47
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	10.37
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.20
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.27
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.11
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	27.40
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.23
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	26.03
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.78
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.34
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	23.27
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	21.14
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	20.07
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.68
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.65
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.08
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.71
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	13.09
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	12.64
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.91
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.64
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	40.62
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	35.86
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.81
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	29.36
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.94
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	28.24
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.04
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	25.31
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	23.16
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.51
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	22.08
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	21.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	16.53
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.48
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.68
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.56
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.31
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	23.90
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	22.81
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.95
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	21.13
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.13
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	19.09
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.75
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	18.63
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	14.45
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	13.63
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	12.73
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	7.00
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.02
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.29
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.99
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.73
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.76
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.05
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	14.54
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.82
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.44
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	13.03
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	12.97
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	11.58
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.18
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	8.27
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.74
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.33
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	30.50
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	22.99
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	20.31
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	20.02
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	15.01
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	14.69
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	14.37
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	13.97
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	13.88
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	11.33

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.