Gene detail

Detailed information of OS493_001568-T1 in Lophelia pertusa

Genomic Location: scaffold_3:4594706...4608861
NR annotation: KAJ7381432.1, hypothetical protein OS493_001568 [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
Q5F415	TBC1 domain family member 23 OS=Gallus gallus OX=9031 GN=TBC1D23 PE=2 SV=1
Q6NRC7	TBC1 domain family member 23 OS=Xenopus laevis OX=8355 GN=tbc1d23 PE=2 SV=1
Q8K0F1	TBC1 domain family member 23 OS=Mus musculus OX=10090 GN=Tbc1d23 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005967 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00566 all species →	RabGAP-TBC	Rab-GTPase-TBC domain	Family	Interproscan
PF19430 all species →	TBC1D23_C	TBC1 domain family member 23 C-terminal	Domain	Interproscan
PF00581 all species →	Rhodanese	Rhodanese-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000195 all species →	Domain	Rab-GAP-TBC domain	Interproscan
IPR035969 all species →	Homologous_superfamily	Rab-GAP-TBC domain superfamily	Interproscan
IPR045799 all species →	Domain	TBC1 domain family member 23, C-terminal domain	Interproscan
IPR036873 all species →	Homologous_superfamily	Rhodanese-like domain superfamily	Interproscan
IPR001763 all species →	Domain	Rhodanese-like domain	Interproscan
IPR039755 all species →	Family	TBC1 domain family member 23	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13297 all species →	UNCHARACTERIZED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0042147 all species →	Biological Process	retrograde transport, endosome to Golgi	Interproscan
GO:0099041 all species →	Biological Process	vesicle tethering to Golgi	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
K22555	TBC1D23; TBC1 domain family member 23	-	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_001568-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

93.2Max TPM

28.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	16.99	23.56
polyp at pH7 6	18	18	20.09	33.34
coral polyp · control treatment	16	16	38.21	93.23
coral polyp · oil and dispersant treatment	16	16	45.93	81.13
coral polyp · oil treatment	16	16	34.27	54.35
coral polyp · dispersant treatment	16	16	24.79	46.53
Polyp	10	10	16.73	31.41

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.56
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.49
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.80
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.78
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.66
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.43
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	17.31
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.82
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.53
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	16.06
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.52
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.44
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.34
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	15.01
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	14.03
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.67
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	13.63
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	12.73
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.34
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.29
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.32
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.98
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	22.46
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	20.34
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.61
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.46
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.31
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	18.24
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.75
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.69
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.15
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	17.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.55
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.14
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.86
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	9.16
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.23
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	48.89
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.93
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.57
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	40.98
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	37.14
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.97
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.68
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.73
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.15
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.77
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	29.20
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	28.62
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	25.99
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	24.05
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	19.43
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.13
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.61
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	57.02
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	53.40
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.19
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.93
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.01
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.65
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.55
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	42.04
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.51
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.55
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	33.11
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.60
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	27.54
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.35
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.71
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.78
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	41.60
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	40.32
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.18
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.91
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.80
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.31
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.47
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.70
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	27.72
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.72
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.14
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.74
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	15.89
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.53
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.25
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.34
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.50
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	33.65
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.58
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.52
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	22.03
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.74
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.20
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	20.60
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	19.72
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	18.93
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.73
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.10
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.23
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	31.41
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	18.02
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	17.20
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	16.79
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.50
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	15.43
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	14.68
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	13.59
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	12.58
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	12.10

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.