Gene detail

Detailed information of CAB4004821.1 in Paramuricea clavata

Genomic Location: pcla8_s005110:11173...13950
NR annotation: CAB4004821.1, toll-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A026290

ATGTTTTTTTTGGTAGTATCATCGGAGGATCCCAGAGAAGAGTGTTCGTTGAATTTGAATGTTGGGGACATTTTAAAAAGGTCAGTACAAAAATCCGAACAATCTAGTGTAGCAGTACATCAAATCGGTTGTGTATGCCACAGCCCGGCAAGGATGTCTTTCTGCCGAGCGGAGAATTTTACTGCGAATGATGTCATTTTATATCTTACTATCTTCCGTCATTGCCGTGTGACCGGCGCAGATCTGGCAGTCTGGGGACGAGCTGCGGACTTGCGGGTGTTGTATTTAATGGATGACGTCATTCTACAAGACAACGGCGAAACGAAGGATGATTTACAAGGCTTATTTAATATCGGGACATTGACTTTACGCAATTTGAAAAACAAGACAATACCCCGTATGTTTTTGTCCTATATTTGGGAAAAAATGGCCGAAATTCAGTTGAGTAAAATACGGTTAGGATCAACTGTGAATATTTTGAAAACAACAATGCCGTATTTACAGTCACTTGAGTTATCTGGAAACGACCTAAGAGCCCTACCAGATTTCCCATGGTGCAACAGGAGTTTGAAACTGCCGAGAAAATTGTCCCGTACTTTCACCATGAACGCGTATTATTCGCAAGGGGCGACAATAAATCCGCATGTATATCGTCGCTTTTACGCAGTTCACTTCAATCCGGGAATACGCGACTTCAAAATTCCTTCGGGTAGTTTGGATAAGATTTCGATACGTGGCGACAATCTGAAGTCTATTGATTCGACGATGTTTCATGGAGTAACGGGTTTAAAAGTTATCGATTTAAGCTTGAACAAACTAAGCCATATTCCTGAGCGCATTTTCGAAAAAACACCAGATGTCGTCTCGGTAAACTTTGCAAATAACAATCTCACTTGGTTGGATGGGAAAACTTTTGAGAACTTGACAAATCTTCGAAAATTGGATGCCGGGCACAACTATATTCACACGATACAAAATGGTTTTCTGTCGGACAAACTGGTGAACTTAGAAGCGATTGAGTTTGAAAATAATCTGTTGCGTGTTATCGAAGCGCGCGCTTTTCCCCGTAGCGTGCTTAATGCGTTGAAGAAAATTAATTTGCGCAAGAATAAATTGCGCGAAGTGCCGCAGTTTGGTTTCTACGTTCGAAATTTGAAGACTTACGACATTTCTGAAAATGGGATAGACTTTGCGGGCTTTGTAAGGACAGTTGATAGAATTTTTATGCCTGACTTTTTATATGTTCACACCAATTCAGGAAGTTCTATCGATACACCAATAAATTTTCGAAATGAAAAAATTCTCAATCTCGAACGCAACGCCATTGAACGTTTCGACTTGACGGAATTCAATAAAACAAGATTGATAACACTCGAGTTCATTTTAAAAGTTTTTACGATAAGTTTAACGGGAAACCCACTTCATTGTGATTGCAAGACGCGTGAATTGCAAATAAAGCTTTTAAATTGGACAAAAGGAAACACTGAGATCACTGAGAAGGATTTTGAAAGTTGGGTATGTCACACACCACCGGAATTACGTGGAATGAAAATTTTAAACGTCCCATCGAAAGACTTAAGATGCGAAAGGCGTTGCGGTAAATGCCCCAAACGTTGTACTTGCTACCGAAGCGATTCCGACTCTGTGACGCTCGTAGACTGTCGGAGACGAAACCTGACGATGCTACCCAGCATACTTCCAAACGGTATGGTTGAATTACGTTTGGAATACAACCAAATCGAAAACTTAACTTTTTCAAAAAACACGGAAAACGTTACCTCGCTTTATGCAAGTCATAACAAGCTACAACGCGTTTCCCTTACTTTAAAGCATTTCCCTTCGAAATTAAACGAAATCTATTTGGATTCAAACAAGCTAACAACACTCCCCAACGGTTTTCGAAATTTCACTCTATCGAGGATAAACTTACAGAATAACTTTTTCACGTGCGGCTGTGAGAATCGCTGGATGAAAAGTTGGTTGAAACAGCAAAGCAAAGCGTTTGTCGGCGGTGCGGAAAGTGTGGCTTGTAGCTCGGGTGGTATGAATCAAGCAAAACCGTTAGTTTCTGTCAAAGATACGGATTTTGTTTGCACAGAAACAGTCAAACCAAACGGCTATAATGTTAATGAGATCAAAGCCATCTCTGCTTACGTTTTGGCGGGATTTCTATTCACGCTTCTCGTAATGGTTGCATTAATTTATCGATTTCGTAAAGAACTTAAACTTGTATTGTATACTCGTTTTGATTGGCACCCGTTTGATCGTGTCGACGATTCCGACCCATCGAAAGTCTACGACGCGTTTGTGTCATTCAACATGTGCGACAAACGATGGGTGATGGAAACACTGCAGAATAAACTCGAAAATCATCATCCATCGTATAAATTATGCATCCACTATCGGGACTTTATCCCGGGGGCACCAATCGCCGAGACTATCCTGGAGAGTGTCAAGAAAAGCCGGCGTATGATAATGGTTTTGTCGCGAAATTTTATTCAAAGCGAATGGTGTATGCTGGAATTCCGGGCGGCACATCGCAGGGTTTTGAAAGGTCGCACGAACTATCTCATAATCGTACTTTTTGACGACGTCAATGTCGACAGCTTGGATGATGAGTTGAAGTTGTATTTGAAGACCAACACGTATCTCAGTGTTCAGAGCAAATGGTTCTGGCAACAATTGAAGTACGCGCTACCACAAAAGAAACAGGAAACGAGTGATGGTTTCCTAGGCAACCAGGCACTCGACTCTGATGAAAAATACATTCAGGCATAA

Transcript

rna-PACLA_8A026290

ATGTTTTTTTTGGTAGTATCATCGGAGGATCCCAGAGAAGAGTGTTCGTTGAATTTGAATGTTGGGGACATTTTAAAAAGGTCAGTACAAAAATCCGAACAATCTAGTGTAGCAGTACATCAAATCGGTTGTGTATGCCACAGCCCGGCAAGGATGTCTTTCTGCCGAGCGGAGAATTTTACTGCGAATGATGTCATTTTATATCTTACTATCTTCCGTCATTGCCGTGTGACCGGCGCAGATCTGGCAGTCTGGGGACGAGCTGCGGACTTGCGGGTGTTGTATTTAATGGATGACGTCATTCTACAAGACAACGGCGAAACGAAGGATGATTTACAAGGCTTATTTAATATCGGGACATTGACTTTACGCAATTTGAAAAACAAGACAATACCCCGTATGTTTTTGTCCTATATTTGGGAAAAAATGGCCGAAATTCAGTTGAGTAAAATACGGTTAGGATCAACtgtgaatattttgaaaacaacaATGCCGTATTTACAGTCACTTGAGTTATCTGGAAACGACCTAAGAGCCCTACCAGATTTCCCATGGTGCAACAGGAGTTTGAAACTGCCGAGAAAATTGTCCCGTACTTTCACCATGAACGCGTATTATTCGCAAGGGGCGACAATAAATCCGCATGTATATCGTCGCTTTTACGCAGTTCACTTCAATCCGGGAATACGCGACTTCAAAATTCCTTCGGGTAGTTTGGATAAGATTTCGATACGTGGCGACAATCTGAAGTCTATTGATTCGACGATGTTTCATGGAGTAACGGGTTTAAAAGTTATCGATTTAAGCTTGAACAAACTAAGCCATATTCCTGAGCGCATTTTCGAAAAAACACCAGATGTCGTCTCGGTAAACTTTGCAAATAACAATCTCACTTGGTTGGATGGGAAAACTTTTGAGAACTTGACAAATCTTCGAAAATTGGATGCCGGGCACAACTATATTCACACGATACAAAATGGTTTTCTGTCGGACAAACTGGTGAACTTAGAAGCGATTGAGTTTGAAAATAATCTGTTGCGTGTTATCGAAGCGCGCGCTTTTCCCCGTAGCGTGCTTAATGcgttgaagaaaattaatttgcGCAAGAATAAATTGCGCGAAGTGCCGCAGTTTGGTTTCTACGTTCGAAATTTGAAGACTTACGACATTTCTGAAAATGGGATAGACTTTGCGGGCTTTGTAAGGACAGTTGATAGAATTTTTATGCCTGACTTTTTATATGTTCACACCAATTCAGGAAGTTCTATCGATACACCAATAAATTTTCGAAATGAAAAAATTCTCAATCTCGAACGCAACGCCATTGAACGTTTCGACTTGACGGAATTCAATAAAACAAGATTGATAACACTCGAgttcattttaaaagtttttacgATAAGTTTAACGGGAAACCCACTTCATTGTGATTGCAAGACGCGTGAATTGcaaataaagcttttaaattgGACAAAAGGAAACACTGAGATCACTGAGAAGGATTTTGAAAGTTGGGTATGTCACACACCACCGGAATTACGTggaatgaaaattttaaacgtCCCATCGAAAGACTTAAGATGCGAAAGGCGTTGCGGTAAATGCCCCAAACGTTGTACTTGCTACCGAAGCGATTCCGACTCTGTGACGCTCGTAGACTGTCGGAGACGAAACCTGACGATGCTACCCAGCATACTTCCAAACGGTATGGTTGAATTACGTTTGGAATACAACCAAATCGAAAACTTAACTTTTTCAAAAAACACGGAAAACGTTACCTCGCTTTATGCAAGTCATAACAAGCTACAACGCGTTTCCCTTACTTTAAAGCATTTCCCTTCGAAATTAAACGAAATCTATTTGGATTCAAACAAGCTAACAACACTCCCCAACGGTTTTCGAAATTTCACTCTATCGAGGATAAACTTACAGAATAACTTTTTCACGTGCGGCTGTGAGAATCGCTGGATGAAAAGTTGGTTGAAACAGCAAAGCAAAGCGTTTGTCGGCGGTGCGGAAAGTGTGGCTTGTAGCTCGGGTGGTATGAATCAAGCAAAACCGTTAGTTTCTGTCAAAGATACGGATTTTGTTTGCACAGAAACAGTCAAACCAAACGGCTATAATGTTAATGAGATCAAAGCCATCTCTGCTTACGTTTTGGCGGGATTTCTATTCACGCTTCTCGTAATGGTTGCATTAATTTATCGATTTCGTAAAGAACTTAAACTTGTATTGTATACTCGTTTTGATTGGCACCCGTTTGATCGTGTCGACGATTCCGACCCATCGAAAGTCTACGACGCGTTTGTGTCATTCAACATGTGCGACAAACGATGGGTGATGGAAACACTGCAGAATAAACTCGAAAATCATCATCCATCGTATAAATTATGCATCCACTATCGGGACTTTATCCCGGGGGCACCAATCGCCGAGACTATCCTGGAGAGTGTCAAGAAAAGCCGGCGtatgataatggttttgtcgCGAAATTTTATTCAAAGCGAATGGTGTATGCTGGAATTCCGGGCGGCACATCGCAGGGTTTTGAAAGGTCGCACGAACTATCTCATAATCGTACTTTTTGACGACGTCAATGTCGACAGCTTGGATGATGAGTTGAAGTTGTATTTGAAGACCAACACGTATCTCAGTGTTCAGAGCAAATGGTTCTGGCAACAATTGAAGTACGCGCTACCACAAAAGAAACAGGAAACGAGTGATGGTTTCCTAGGCAACCAGGCACTCGACTCTGATGAAAAATACATTCAGGCATAA

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
Q8SPE9	Toll-like receptor 4 OS=Pongo pygmaeus OX=9600 GN=TLR4 PE=3 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
PF13306 all species →	LRR_5	BspA type Leucine rich repeat region (6 copies)	Repeat	Interproscan
PF01582 all species →	TIR	TIR domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan
IPR000483 all species →	Domain	Cysteine-rich flanking region, C-terminal	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
IPR017241 all species →	Family	Toll-like receptor	Interproscan
IPR035897 all species →	Homologous_superfamily	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Interproscan
IPR026906 all species →	Repeat	BspA-type LRR region	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
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

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 CAB4004821.1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of CAB4004821.1 across 21 RNA-seq samples of Paramuricea clavata. 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.

21Samples

14TPM > 0

4Conditions

8.5Max TPM

0.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	0.95	5.02
apical branchlet · Temperature treatment at T0	6	3	0.03	0.07
apical branchlet · Temperature treatment at T25	5	3	2.01	8.54
apical branchlet · Control at T0	4	3	0.11	0.21

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.02
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.48
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.14
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.04
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.01
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.07
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.06
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.02
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.54
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.14
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.38
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.21
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.15
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.09
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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.