Gene detail

Detailed information of OS493_026959-T1 in Lophelia pertusa

Genomic Location: scaffold_142:835852...846131
NR annotation: KAJ7371314.1, 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
B6CJX2	Myeloid differentiation primary response protein MyD88 OS=Cercocebus atys OX=9531 GN=Myd88 PE=2 SV=1
B3Y680	Myeloid differentiation primary response protein MyD88 OS=Gorilla gorilla gorilla OX=9595 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
IPR035897 all species →	Homologous_superfamily	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Interproscan
IPR000157 all species →	Domain	Toll/interleukin-1 receptor homology (TIR) domain	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_026959-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_026959-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

151.5Max TPM

72.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	57.03	82.48
polyp at pH7 6	18	18	59.54	78.43
coral polyp · control treatment	16	16	82.59	125.66
coral polyp · oil and dispersant treatment	16	16	100.13	151.47
coral polyp · oil treatment	16	16	79.96	138.46
coral polyp · dispersant treatment	16	16	74.03	145.71
Polyp	10	10	44.39	90.57

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	82.48
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	76.40
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	73.96
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	72.95
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	62.11
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	60.52
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	59.89
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.74
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	57.17
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	56.76
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	50.75
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.31
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	49.08
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	48.31
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	46.68
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	44.55
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.37
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.57
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	78.43
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	76.61
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	75.52
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	70.38
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	68.70
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.88
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	67.16
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.36
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	64.18
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	60.54
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.60
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	57.15
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.09
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.00
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	44.81
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	42.69
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	35.85
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.79
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	125.66
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	112.73
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	106.65
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	97.41
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	96.68
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	93.62
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	82.91
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	81.14
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	80.18
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	79.21
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	77.11
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	71.88
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.67
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	60.03
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.92
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	31.60
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	151.47
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	132.49
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	123.58
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	111.91
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.98
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	106.25
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	105.53
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	103.64
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	103.18
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	98.92
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	92.13
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	89.66
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	86.42
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	68.39
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.91
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	54.57
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	138.46
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.78
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	96.67
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	93.24
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	91.87
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	89.41
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	84.93
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	81.80
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.68
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	80.29
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	76.63
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	73.47
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	72.49
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.71
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.40
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	25.45
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	145.71
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	109.51
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	94.26
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	87.72
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	86.79
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	79.53
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	74.21
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	73.82
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	70.48
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	67.61
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	66.93
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	64.42
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	62.61
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.96
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	34.23
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	21.67
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	90.57
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	62.03
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	58.95
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	43.45
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	41.65
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	32.92
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	32.02
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	31.69
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	29.59
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	21.01

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.