Gene detail

Detailed information of OS493_026949-T1 in Lophelia pertusa

Genomic Location: scaffold_142:630690...643852
NR annotation: KAJ7371305.1, Myeloid differentiation primary response protein MyD88 [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
A8QMS7	Myeloid differentiation primary response protein MyD88 OS=Takifugu rubripes OX=31033 GN=myd88 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001787 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00531 all species →	Death	Death domain	Domain	Interproscan
PF13676 all species →	TIR_2	TIR domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017281 all species →	Family	Myeloid differentiation primary response protein MyD88	Interproscan
IPR000488 all species →	Domain	Death domain	Interproscan
IPR011029 all species →	Homologous_superfamily	Death-like domain superfamily	Interproscan
IPR000157 all species →	Domain	Toll/interleukin-1 receptor homology (TIR) domain	Interproscan
IPR035897 all species →	Homologous_superfamily	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15079 all species →	MYD88	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0002755 all species →	Biological Process	MyD88-dependent toll-like receptor signaling pathway	Interproscan
GO:0043123 all species →	Biological Process	positive regulation of canonical NF-kappaB signal transduction	Interproscan
GO:0070976 all species →	Molecular Function	TIR domain binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	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_026949-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_026949-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

79.5Max TPM

31.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	25.27	38.60
polyp at pH7 6	18	18	27.57	40.81
coral polyp · control treatment	16	16	44.95	79.53
coral polyp · oil and dispersant treatment	16	16	41.80	59.80
coral polyp · oil treatment	16	16	34.46	57.44
coral polyp · dispersant treatment	16	16	26.66	40.77
Polyp	10	10	18.59	29.59

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	-	38.60
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.50
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.49
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.01
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.83
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.80
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.58
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.44
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.62
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.59
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.31
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.55
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	22.08
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	21.45
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.89
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	19.20
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	11.66
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	10.31
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.81
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	40.62
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	38.16
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	37.40
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.61
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.91
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	33.22
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	32.04
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.11
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	28.67
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.34
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	24.31
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	21.62
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	16.17
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.98
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	15.36
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	14.63
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	13.30
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.53
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.73
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.48
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	59.37
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.53
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	52.92
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.34
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	45.12
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	39.89
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	38.42
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.46
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	35.98
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.12
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	22.45
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	16.91
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	10.90
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	59.80
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	58.85
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.67
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	52.44
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	51.86
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.54
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	48.02
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	47.60
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.56
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.77
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.73
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.39
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	31.95
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	26.58
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	19.86
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	10.14
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.44
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	46.32
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	45.23
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.84
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.73
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	42.40
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	38.95
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	36.09
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	35.42
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	34.44
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.91
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	28.16
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	20.56
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.58
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.24
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	17.13
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.77
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	37.15
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	36.62
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.52
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.15
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.02
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.31
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.91
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	28.18
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	27.94
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	25.28
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	23.76
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.20
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	15.02
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	5.20
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	3.62
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	29.59
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	24.98
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	22.48
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	20.25
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	19.17
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	16.49
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	15.42
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	15.09
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	12.15
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	10.30

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.