Gene detail

Detailed information of OS493_005620-T1 in Lophelia pertusa

Genomic Location: scaffold_11:3240935...3249507
NR annotation: KAJ7365511.1, hypothetical protein OS493_005620 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

OS493_005620-T1

ATGGATAACGCCGACTTGGAAAAGCTTTCTATTTCTCCTGGAAAACTAACCCCGAAATTCCATCCGAACACCACTGAATACTCGGTAACTCTTGGAAGTGATGTTAAACAGATTAAAATCGATCCACTTACAAGCGATTCTGGGGCATCTTACTCTATTTCGGGAAGTGGTGGTGGGAAAACAGTAGCTCTCAAAGAGGGAGAAGTTACACCCGTGAAAATAGAAGTAAGTGCAGAAGATGGGAGCACGATCAAGAACTATTTCATTCAAGTTACGAGATTGTCTGCAAGTGACGCGTCGCTCACCGATCTCAAACTTTCGGTCCTCGGAAGTCTTTCTCCAAATTTTGCTTCCAATGTCACAAGTTACTCTACCTTCGTGCCGTTTACTTGCTCGTCCGTTGAAGTAATTCCCGGCGTGGCTGATAAAAAAACCGTAGTGACAGTAAACGGTGGTGAATCGAAAGATCCTATAGCTTTAAATTTTGGCGAGACGGTCGTTCAAGTGGAAGTGACCTCTCCAGATGCAAGCAACAAACGAACGTACGCGTTGGTGATTTCGAGACTGAAGCTTTCAAGGCCGATAAAGTTTTCAGATGAAAAGCAGCAATTGAAGTTTGAATGCCCTGTTTGTCTGGGCGTAGTTTACCGGCCTAAATCGATCAAGGAAAGTGAACCGAAGCATGTGTTCTGCAAGGGTTGTATCGATGAACTTACACGAACCTCGAAGCAAGACCCCTTGGACGGCTCTCCGCTAGTTGATCTGTGGCGCGTTGATGAATACGATCTAGACAAGGAATTATCTTCCCAAGCAGTGTTGTGTGTTTATAAGCACTGGGGATGTTGTGAGGAATTGAAGCTGTGTGAGCTTGGTCCTCATGTGAAGCAGTGTGAATTCAGGCCTGTTGTTGTGGAGAAGTCTGCGGAAATGGTCCCAGCCAAGGATTTAGAGGAAAAATCAAAGGAGGCTTGTAAAGGATGCCCAGATTGTAACCGGCCAGTCCGAACAGCTGAGCTAGAGGAACACAAGACCTACATGTGCACCAGCAAACATCCCAACACAGGTGTCAAGCACAAGTCTGAAATCAGATCATGGGAGAAGAAACTTCAGCAAGAGACAAGTGAAAAATCTGCTGACAAGTTGGTCAAGACAGCTGAAGAGCAAATTAATGAATGCTTCAAGGTCTTGCCTCAGCATGGTAATGCAGGCCATTTTGACGGAGACGTTTCACCACTGAGGTACCTGGAAATGGCTGCAGAGTGGTTTGCCACAGCAATCAAGTTGTCGCCAAAAAGAGCTGATCTTCACTTTCAGCTGGGCCAGGTTTTAGAGGAACAACATTATGTACAGGATCTGTATGGGATCAAACCTCCAAAATCTTCTGACGATTATGATGAAATGGATTTTAACATGAAATCCAAGGAGAGTTCAAAGGAAGATGACATTCAGGCCATCTGTGAGATGCGTGGTGCAGGACGGAACGCACCTCTAGCCCTGCAGCTCAAGGCAATTGATGAAGAATATCATTATCTCTTGGACCAAGGACAGTCTGACAGGGTTGACTATGTTCAAAAGTTGTATGCATGGAAATCTAAACAGGCTACACAGAACAAAACAGCCCAGCTGGCTACCAATGAAGAAGAGCTTCTTGGAAAAGCATATCTCAAGTACTTAGATGCTCTGGCCAATGGAACTGACAACCATGTGTACAACTTGCATGTCGGTAGAATGCTACTCCTTCAAAGCAAACCAGAAGAAGCTGTATTGCGTCTTCAAGTTGCTGTGGGATTGAAGCCAACTAATATTGACGCAAGGTTTTTCCTTGGGTTGGCTCTTTGCCAACAAAAAGGTGGAGCAGGCAAAAGGAAAGAAGAAGCTGTGAAATATTTGTCTGAAGGAATTGAACATCTGTTGAACCAAATGAGTGCTGACTCAAATGACCCTAGCAAGGATCCTGAACAATGGCAACAGACAACTCTCTCTTCCAATGACTTGTTGAGACCTGACAACGTTCAGTGGCTGCAAGGATGTGGTCTTCTCGGCAGCTTATGTAAACAAATGCCAACAACACCATCAGGTGTGATGTCGACAGATATTGCTTTGCATACGTCTGCTTTGTTGGCGTCGGATGTCTTGTCGCGTCTCGTAGCTAGAGGGGACACATACCATCAAGTTGAGTGGGTCTTGTTTGAGACCCATTTCACACTCCTTCAAACGATGCTGGATAGCGCAAAGCGGAAAGGAGATGGAAAGAATGGCGAGATTTCTCGACGTTTCTGTGAAAATTTGTCTGGTTTGCTTAACTGCTCAACCATTCCACCTGGAAAGCAAATTCTTGAATTGCAAGAAAAGACCTGCCAGCAAGCTGTTCTGCTTCAACCGTGTAATAGCCGTTCTCTTTATCGCCTGGGTGACGCTCAACTAAGTTGCCATGACAATGACGACCCTACCTCGGCTAATGCCAAACAGATTCTCCAAGACGCCGAGCTGAGCTATCGAGCAAGTATTGAGCAAGAAGGGTGTCCATCAGTAGGTGGGGAGGCCCCAGGTAAGGTCAGTGAACAGCGATGGTTCAAAGAGCAAACAGAAAAGCCAGTGGCAGAAAAGAAGGGAGCTGCAGGAGGAACCCCTCAAAAAATTGCCGCTGCACCAGCTGCTAAGGGAGCCTCCCCAGCTGGGCGAGGTGGGACCCAAGCAGGAAGAGGTTCGTCTACTACAGCTCGTGGTGGAGCAGCAGTGAGAGGCAGAGGCAGTACTCCTCCCACTCGAGGCGGAGCCACCACTGCAGCAAAGGCACCAGCTGGTGGAACTCGGGGCAGGACATCTCCTACGAAGCCTGCTGGTGCACCAGGGAGGGGTGCGTCTAGAGGAGGAACTACTGCAGCAGCCAGTAGAACATCAGCATCAAAACCGTCAACTTCAACACCTACAGCTCATAAATCAGGTGCGTGTTCTCCTACAAAGCAGCCAACTACAACTAAACAATCAACACAAGCAAAACCTCCAGCAACTTCAGCTCCAGTCAAACCTGCCGAGCCCAGTCCTGCAACTGAACCTAAGCCGAGTGGACCACTCAACAAACCTTCCTACCACGCCCGTCTGGGATTGGCTCGCGTTTTGATGCGAAAAGGCGGTGACAGCATCAACGAAGCCCATAAATTATATGAAGAAGTGATCTCAATGGCGCCAGCGGTTCACGATGCTTACATCGAATTGGCGGACTCCTTGATCAAGGCAGACCCCATGAAGGCCGTCGACACATACAGCAAGTACCCTTTTCAGGAGCCACTGACGTTTGATGATGCATACATCCATGGGGAGATGGTTCGTTTGTTGATGAAGAATGAGAAGTATGATGATGCCAGACTGAGTCCAAGTATGGTGTCTCTTGGGAAGGTTATGGGTCTTACCGTGTTGGAGAAATACGTTGACACACTCGACAAGACCTTCAAGTACAGCAAATTGCTTATGCAAGTTTATGCTGGGGTGCATGGTAAAAGTGTTGATGATCCAGATTTGCAACAGTTTTTTAAGTTTAAATGTTGGGTTTAA

Transcript

OS493_005620-T1

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006959 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12733 all species →	Cadherin-like	Cadherin-like beta sandwich domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR025883 all species →	Domain	Cadherin-like beta sandwich domain	Interproscan
IPR051438 all species →	Family	RNF E3 ubiquitin-protein ligase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46016 all species →	ZINC FINGER, RING/FYVE/PHD-TYPE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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_005620-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_005620-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

12.9Max TPM

1.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	2.05	3.85
polyp at pH7 6	18	18	1.79	3.66
coral polyp · control treatment	16	16	1.85	10.41
coral polyp · oil and dispersant treatment	16	16	1.42	12.92
coral polyp · oil treatment	16	16	1.49	3.12
coral polyp · dispersant treatment	16	16	1.04	2.40
Polyp	10	9	0.90	2.31

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.85
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.62
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	3.26
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.87
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.51
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.43
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.36
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.35
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.35
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.09
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	2.08
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.48
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.16
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	1.03
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.98
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.94
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.88
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.74
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.66
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	3.28
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.89
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.87
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.74
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	2.50
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.97
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.67
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.60
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.54
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.52
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.40
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	1.12
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.99
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.78
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.70
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.62
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.38
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.41
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	2.57
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.91
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.89
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.73
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.59
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.36
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.31
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.27
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.18
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.05
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	1.02
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.83
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.66
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.43
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.31
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	12.92
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.48
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.19
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	1.12
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.92
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.85
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.75
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.58
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.55
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.53
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.48
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.41
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.25
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.19
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.18
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	3.12
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.57
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	2.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.73
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.72
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.59
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.58
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.58
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.45
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.18
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.14
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.10
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.91
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.77
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.70
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.50
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.40
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	2.07
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.92
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.83
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.20
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.11
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	1.07
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.89
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.88
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.73
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.62
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.58
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.51
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.44
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.23
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.14
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	2.31
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	1.61
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	1.60
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	1.16
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.76
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.58
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.35
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.34
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.29
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	0.00

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.