Gene detail

Detailed information of OS493_016700-T1 in Lophelia pertusa

Genomic Location: scaffold_52:26503...29738
NR annotation: KAJ7372782.1, Transport and Golgi organization protein 6 [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
Q8C3S2	Transport and Golgi organization protein 6 homolog OS=Mus musculus OX=10090 GN=Tango6 PE=1 SV=1
Q9C0B7	Transport and Golgi organization protein 6 homolog OS=Homo sapiens OX=9606 GN=TANGO6 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004055 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10304 all species →	RTP1_C2	Required for nuclear transport of RNA pol II C-terminus 2	Repeat	Interproscan
PF10363 all species →	RTP1_C1	Required for nuclear transport of RNA pol II C-terminus 1	Repeat	Interproscan
PF02985 all species →	HEAT	HEAT repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019414 all species →	Domain	RNA polymerase II assembly factor Rtp1, C-terminal domain 2	Interproscan
IPR039600 all species →	Family	TANGO6/Rtp1	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR021133 all species →	Repeat	HEAT, type 2	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR019451 all species →	Domain	RNA polymerase II assembly factor Rtp1, C-terminal	Interproscan
IPR000357 all species →	Repeat	HEAT repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20959 all species →	TRANSPORT AND GOLGI ORGANIZATION PROTEIN 6 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0009306 all species →	Biological Process	protein secretion	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_016700-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_016700-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

18.7Max TPM

4.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	4.40	7.17
polyp at pH7 6	18	18	4.11	8.64
coral polyp · control treatment	16	16	6.13	18.69
coral polyp · oil and dispersant treatment	16	16	4.27	9.24
coral polyp · oil treatment	16	16	6.29	16.87
coral polyp · dispersant treatment	16	16	5.65	9.61
Polyp	10	10	3.35	5.85

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	-	7.17
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.90
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.89
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.86
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.48
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	6.04
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	5.31
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	4.32
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.81
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.52
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.30
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.22
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.08
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.03
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.62
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.50
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.57
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	8.64
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	7.90
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.90
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.72
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.63
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	5.33
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	4.50
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.97
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.85
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.71
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.53
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.12
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.38
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.31
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.19
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.19
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.01
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.11
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	18.69
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	14.26
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	8.21
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.50
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.40
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	6.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.44
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	5.40
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.45
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.29
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.12
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	4.04
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	3.06
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.60
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.23
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.09
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	9.24
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	8.59
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.77
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	6.51
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	5.03
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.82
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	4.55
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.30
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.19
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	3.01
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.97
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.93
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	2.25
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.99
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.91
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.17
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	16.87
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.48
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.08
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	11.01
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.98
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.64
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.10
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.04
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	5.03
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	4.50
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.72
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.65
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.33
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.22
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.60
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.38
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	9.61
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	7.14
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.95
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.74
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.31
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	6.23
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.80
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.73
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.61
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.60
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.07
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.88
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.86
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	4.39
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.87
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.64
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	5.85
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	5.47
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	4.33
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	3.64
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	3.33
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	2.79
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	2.67
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	2.31
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	1.75
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	1.32

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.