Gene detail

Detailed information of OS493_027529-T1 in Lophelia pertusa

Genomic Location: scaffold_150:893169...894840
NR annotation: KAJ7326575.1, Transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) [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
Q2KII4	Elongin-C OS=Bos taurus OX=9913 GN=ELOC PE=1 SV=1
Q15369	Elongin-C OS=Homo sapiens OX=9606 GN=ELOC PE=1 SV=1
P83940	Elongin-C OS=Mus musculus OX=10090 GN=Eloc PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008238 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03931 all species →	Skp1_POZ	Skp1 family, tetramerisation domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011333 all species →	Homologous_superfamily	SKP1/BTB/POZ domain superfamily	Interproscan
IPR039948 all species →	Family	Elongin-C	Interproscan
IPR016073 all species →	Domain	SKP1 component, POZ domain	Interproscan
IPR001232 all species →	Family	S-phase kinase-associated protein 1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20648 all species →	ELONGIN-C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0070449 all species →	Cellular Component	elongin complex	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
K03872	ELOC, TCEB1; elongin-C	-	DNA repair and recombination proteins	ko03400	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_027529-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

202.6Max TPM

87.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	69.52	145.13
polyp at pH7 6	18	18	79.08	116.74
coral polyp · control treatment	16	16	101.22	202.64
coral polyp · oil and dispersant treatment	16	16	117.27	179.88
coral polyp · oil treatment	16	16	84.49	132.89
coral polyp · dispersant treatment	16	16	77.85	163.28
Polyp	10	10	88.80	162.62

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	145.13
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	113.62
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	79.16
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	75.38
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.32
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	69.10
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.53
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	66.20
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.96
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.59
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.93
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.40
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.90
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.78
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	55.44
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	52.53
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.93
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.45
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	116.74
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	113.39
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	98.43
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	88.78
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	86.29
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	83.81
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	81.36
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	79.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.21
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.37
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.63
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	74.15
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	73.61
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	69.46
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	65.06
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.09
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.98
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	51.22
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	202.64
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	178.58
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	126.16
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	113.82
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	110.52
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	108.72
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	104.20
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	98.91
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	87.14
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	86.80
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.71
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.07
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	84.57
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	51.63
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.80
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.18
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	179.88
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	145.10
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	142.16
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	133.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	132.61
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	128.13
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	120.08
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	119.66
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	114.07
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.08
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	104.58
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	103.40
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	97.20
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	87.46
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	81.33
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	76.53
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	132.89
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	112.71
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	105.11
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	103.48
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	99.41
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	98.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.86
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	92.61
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.97
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.24
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	78.75
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	71.70
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.45
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	59.06
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	54.64
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.84
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	163.28
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	116.92
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	105.75
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	96.72
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	91.86
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	81.55
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	71.70
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.51
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.42
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.39
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.88
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.87
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.62
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	57.38
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	43.59
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	10.22
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	162.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	136.13
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	113.09
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	96.40
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	95.94
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	92.90
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	67.35
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	46.55
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	41.41
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	35.61

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.