Gene detail

Detailed information of OS493_014970-T1 in Lophelia pertusa

Genomic Location: scaffold_43:1381813...1384731
NR annotation: KAJ7392032.1, axis elongation [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

OS493_014970-T1

ATGGCACACTTCTTTGTATTGCCTCGTACTTTGGTTTGCGTATTGTTGGTAATGGCTTCGAATGGCCACGAAGAGAGCGAACACGCGACAGAACTCTTGCAGTGCCTCGGCAAAACCGATTCATCCGTTTTCGAAACAAGACAAGGTAATGAAGTTCTTAGTAAACAGCTGTATTGCGAGATTAAAAGCGAACAGTCGCTAGTTAAACACAACTTTGATATTGCTGCTGTAGTGCAGACAAGAATTCCAAATGACACCTTGCTTTATTTGACCGTGCATATAAAGTGCTGCACACCGACAAAGCTAGTTTTTACAAATTCGCAGACATTGATTAACAAAAATATTATGTTAAATTTGATGTTTGCTGGACCATGCATCGTTTCAATGCAAAATCTAGCTGTGTGGTCAAACGTGACCGATTTTCACGGTATTGGGTTTAGAGGAGGTGTTCATGGACATAACCCAAACCTTATAAAGGAAAATGGAACTTTGGAAAGAGAGATTCAAACACTGTCAGCCATGACATTTTACAACGGAACCGCTCGAGAAATATTCAACACATTTTCTAGTGCCGAAAATGCGTGGCCGAGAATGGCAGAAATTGGATTGTCAAATCTCTCGCTTGAAAGCATTCCAGAAAAATTGCGAACGATGATGCCCTTGTTACAAACACTCAATTTACAGTCTAACAAATTGACACAACCACCCGACTTTCCTTGGTCCAATTCTACACTAGAATTGCCCCGTGGTTTGAGAAGAAGGAAACATTTTAACGATAAGATTAACAGTCTTGAAGGCATCAAGATTGATGCAAACATTTATTGTCGAGTTTTGAGACTAGATGACAATAACATCGAAGACTTATCGTCTCGAGAGTTCAGAGGATTTCTGCATAAACTGTCTCTTTCGAGAAATGGTTTGCGAAACGTTAGGCCAACGTGTTTTCGCAATTTGAACGGAATTCAAGCGATTGACCTCAGCAAGAATAGGTTGAAAGATTTACCTCCACAACTGTTCCACAGATTAAACTCGTTGCTGGAAATTAGACTTGGAGAAAATAAGCTATCAATCGTCCCACCGGAAATATTTAAAGACTTAAAAAATATCCGAAAGATTACTTTAGATCATAACAACATTAATATTATTTCTAGTGGATTGTTTAACACATTAGACAACCTTGAGGTTGTGCATTTAGAAGGTAACAAAATTGCGAATATTGAAGAAGGCGCCTTCTCAAATAACTCGGTTTTGCGTGAGGTTTACCTTCAAAGCAACAATCTCACCGACGTTCCTCTTGTTATATTTCGGTTAAGAAATGTGTCCACAATTGATATCTCCTTCAATATGTTGAAGTTCCAAGACCTTCTCAATGTTATCGAAAGTTTGAGTGAAGATACATTTCCAAGTAATATTTCTTTGAAAGACACTGAGCCCAGATTGCTCAATTTGTCCAATAACAACTTTACAACGTTAGATATTCACGGCTTAACTGAACTTAACGAAATTAAGTTTTCTCGCTTTCTGGAAATGTACGAGATCGAGTTAACAGGGAATCGTTTGACCTGTGATTGCAGCATATTGACCATCAAGCGTAAGATAGGATTTCTCTTGCAAAATAATCCTTCCTGGAAAACACGGTTTAAAACATGGAAATGTGCATGGCCAGAAGAACTAAAGGACAGAAACATCCTGGAAATTAACGAGAATCATATTATTGCGCAAAAGAAGCTAGAGTACTGCCCTGTCGAATGCTCTTGTTTCGAGCGATGTATGGATCAAACTGTTGTCATCGATTGCGAAGGAAGAAACCTGACTAAAGTACCCAGAATACCATCACGTGGTCCACTGATCGAGCTTAACTTAAGAAACAACAATATCCGCGATATTCCAGTGTATCCTTACTTCAAAAACTTGCTAGCTTTGTATTTGACAAACAACAATATCCAACAGTTTAATGCGATGGCGGTGAACAATTTCAAACGGATACGAGTTCTTCATATCGACTCGAACAACTTGTCAAGCTTACCAAGAAATATCGAGGAGCCTGGTTTCACAAATCTTGCGTTGCATAATAACGCATTCAAGTGCAGCTGTAATTTAAAATGGATGAAAAACTGGCTGCAAAAACTCCATCATAGGAATCAGGTTAAAAATATTGAAAACGTTCTTTGTCAGTCGGACAGCGCCGAAGGAGTGAAAGCAATTTATACTTTGCCTGACGAGAATTTCGGTTGCAACGGAACGGCGGAATACAAAACTGTGACCAATATAATACAGGAAAAAACGTCCACAATCATAGCGGTTACCCTCGGAAGCTTGCTTGCCATGACCTTGATAATTTTTATCCTGCTACTCAAGTACCGAAGAGTAATGAAAGCCTTCATGTATGCCCACTTCAATTGGCACCCGTTTGACCACATAGATGACACGGATTCAAGCAAGATATACGACGCGTTTGTATCTTACAGCGAAAAACAACGCCAGTGGGTTGTAAACACTCTGCAAGAACGACTCGAAAATCACCACCCTCCTTACAAACTATGCATTCATCACCGCGACTTTGAAATTGGTGCACCAATTGTGCGGAACATTTTGAACAGCGTCGAACAAAGTAAGCGCATGCTCATGGTACTATCTCGCAACTTCTTACAGAGCGAGTGGTGCATGCTGGAGTTTCGCACGGCACACCACAAAGCGCTGGAAGATCGCCTTAAACTAATAATCATTATGTTTGATGACGTCAGCATGGCTGAGTTGGATGAAGAAATGAAGCTGTACATGCGCAATAACACGTATGTCAGTGTCAGCGACAAGTGGTTCTGGGAGAAGTTGATTCACGCGATGCCGCAAAGCCCGGTCAGGGAACTGGAAGAAAGATCCAAGCACGACTATGATTTGATCGAAAGTCGTACGAGTTGA

Transcript

OS493_014970-T1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P08953	Protein toll OS=Drosophila melanogaster OX=7227 GN=Tl PE=1 SV=1
Q9V477	Toll-like receptor Tollo OS=Drosophila melanogaster OX=7227 GN=Tollo PE=1 SV=1
Q689D1	Toll-like receptor 2 OS=Canis lupus familiaris OX=9615 GN=TLR2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003005 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13855 all species →	LRR_8	Leucine rich repeat	Repeat	Interproscan
PF01582 all species →	TIR	TIR domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035897 all species →	Homologous_superfamily	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR000157 all species →	Domain	Toll/interleukin-1 receptor homology (TIR) domain	Interproscan
IPR003591 all species →	Repeat	Leucine-rich repeat, typical subtype	Interproscan
IPR000372 all species →	Domain	Leucine-rich repeat N-terminal domain	Interproscan
IPR000483 all species →	Domain	Cysteine-rich flanking region, C-terminal	Interproscan
IPR017241 all species →	Family	Toll-like receptor	Interproscan
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24365 all species →	TOLL-LIKE RECEPTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0002224 all species →	Biological Process	toll-like receptor signaling pathway	Interproscan
GO:0004888 all species →	Molecular Function	transmembrane signaling receptor activity	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006954 all species →	Biological Process	inflammatory response	Interproscan
GO:0006955 all species →	Biological Process	immune response	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0038023 all species →	Molecular Function	signaling receptor activity	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K18809	TL; protein toll	-	Toll and Imd signaling pathway	ko04624	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_014970-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

82TPM > 0

7Conditions

1.1Max TPM

0.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	14	0.09	0.27
polyp at pH7 6	18	11	0.06	0.18
coral polyp · control treatment	16	15	0.19	0.76
coral polyp · oil and dispersant treatment	16	9	0.14	0.46
coral polyp · oil treatment	16	13	0.16	1.08
coral polyp · dispersant treatment	16	14	0.31	0.84
Polyp	10	6	0.09	0.59

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	-	0.27
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.19
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.16
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.16
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.14
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.14
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.13
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.10
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.09
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.08
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.05
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.05
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.03
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.03
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	0.00
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.18
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.17
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.15
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.14
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.12
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.12
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.10
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.05
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.04
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.03
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.01
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	0.00
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.76
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.63
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.33
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.31
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.26
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.14
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.13
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.09
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.09
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.08
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.07
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.06
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.04
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.01
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.01
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	0.00
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.46
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.45
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.31
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.29
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.19
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.14
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.10
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.01
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	0.00
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	1.08
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.28
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.23
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.22
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.21
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.20
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.10
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.09
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.08
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.04
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.03
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.02
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.02
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	0.00
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.84
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.61
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.59
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.55
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.43
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.32
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.25
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.25
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.20
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.16
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.15
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.12
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.09
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	0.00
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	0.59
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	0.18
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	0.06
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	0.02
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	0.01
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	0.01
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	0.00
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	0.00
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.