Gene detail

Detailed information of CAB4004575.1 in Paramuricea clavata

Genomic Location: pcla8_s005039:10773...14390
NR annotation: CAB4004575.1, Low density lipo receptor adapter 1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A062087

CGTTGAACCACACGTACGACATTTTGCAAAGACGACTCGAGACCGAAGTTTGAAGTATGCCTAAAGGAGGACACGTCCGCTTGACCGGTGAAGAATGCGACGAGAAGGACGAAGCTATTGCGGGAAAGAGCTATCAGGTCCGCTACTTGGGTTCCAGCGTTATAGTGAGCTACAACGGTAAAGGCAAGGGGTGTACGGACGCGGCTGTACGCGAGATATACAGTAGGTACAGTACCAAAAACACTGTGAAGAGTCTCCCGAAACGTGAACTATTCGTAAGCGCTAATTGTGTTTCATTATATGCTCCTGTCGAAGAGGTTGTTATGTTCAGATTCCTGACCGTCAACATTACATTCTGCAATACAAACGACGAAAATCGCAATGCCTTCGCGTTTGTGGTCAAGGAATCGACGAACGTGTTCCGTGCTCACGTTCTTCACTGCGACAGCCCGACGCAAGCAAATGATATTTGCGTGGCAATGCATCAGGCATTCATTGTTCGATCTGCGTTGTTTCAAGCGAAACGTGTGGACCGCGCAGGATGGGCGAACGGCTTGCTGTCCTCGCAGGAGAAGCTTGTGGCAAGCGCGCAACAAAATGGCGAACAGCGCACTGGCAAGACCAATGGAAACGGAGTCCACGACGAAATCGATTCGAATAACAATTTTGGGGCGTTTGCGTGCGCTGTTGTGCTGCCGTGTCCGAGCGACATCTGCAATGAATCTAAGAACAATAACAATGTCGATAATCCGAACCTAACACGCTATCAGGGGAGGTTTTCGTTAGCAACGATGCTACTTGAAGGAGGAAAAAACCGCAGCAGAAGTCATAGCTTGCCTTTCCAGATCCAAAACTCGTGGGCAGCGAGCAATGGGGAGTGGGGATGCTTTCAGGGCTCGGAGGAAGACGATGTTGATGATTTTAGTTCGTTTGCACGCGAGAGATCGTCTTCCGTGGGACTACTTATGGCTGAATGAGGTATTTTCTATGATAGACAATGCACTTGAAACGATGGTGAGGGGAATTAACCTTGTTATGATAGATAATATTACACTTGGAACCGTACTAAGCCATGAACTAAATGAAAGGTAATTACCTAGTTAGATACTATTTCATTTTGGAACGGGGGTATCATATAGGTTATCACCATATTAGATAAATATTATAGTCGGAACATTATTGACCATGAAATTAACTATTATTAACCAATTACTATGAACAGAAATGTCGTATAAATAGCTGGAATATTTTTTAGCGAAGTATTAAAGGTAATTACCctattataattaaaatattataattggAACTATATTAATAAGTGATGGTAATTACCCTAATACCATGCATTGAATTAGCTGGAATAGAAATTACGCGAGGATTATTAATATCTCAATACGGTAAATCCCGCATATAAGAATCGTTTTACTTTAACAAGCTATCTTATTAAGTTTAAACtaaagaaaattttggaaaaatcaGACAATTTTTGCCATGAGAATTTTATGGGTGGGTTTTAGTAGGTGCTTTGTATATGCTGCCACGTAGACTAGACCTGGAGAGTGGTTAATGTTCCTCCGACCCTGAATTTGcttttttcaaatgttcctcaaatTAAAAGTGCGGAAAAACAATGGGAAATTCAATCGTACTTAAACCATTGTGTTGCAACAACAAAGCGTCTCAAATGACAGATAAGGAAGTAAAATTGATCCCATAAGAATCTCCCATAACGCCTATGTGTGATtgtgtgaaaaattgaaaatgttcttcaaccttcttgccaaaacaaatgtTCCCCAGGATCCCGAGATCAAATGTATTGGCATTTATGAAGCGAGAAAACGAAGCCAGCAAAACAAGGCGTCTTTTCCTGTTAAAATTGACCAATGTATGCAGTATAGATCCTTTCCTTGTTTACTTTTTAGGCAGGCGTTTTTAGGCAGGTTTTAGAAAGCTTTcaggaaaatattttaaaatcttttaGTCACGAGAGCTTCGTAGTTGCGTCGGACATGCTTGTTGAATCACAAATTGAGAATATAGtctttatatataattggaatttgcctgccagcaaaatataTTAACAAGGCAAGGATCTATGGATttttcaactacctgaaaaagaagaCAATTTATTGAATGCTTCAGTTTTTCAGACGTCTTATCTTACAGCGCACTCGAAATGTCTGTGTTTGTGGATTCAGCCAAATGCAAAAAATCGCTCAGTTCAGTGAGTTCACCTGTTTGACCCTTGCTTTGAAAGCTGGTAAGATTTAAACCCGCAGATTATGAATTTAAGCACAAACGTTTTGGTGATAACAAATTCGGAACTTGTTCCCACAAATCCaattaataaaaattcagttttCTGACGCGAGGCCAAGATCAGAACGTGGGACTTTTCATGTGCCAAACGCATTAAATGCAAATGAGCTCAAAACAAAATCTCGGGTCCTTCACATGACAGCAAGACGCTCGAACTAATCCTGAAAAGTGATGAAAAAGCACATAGACCGAAACAGTGCACGCGGGTTTCATATTAGGTTTTCATGTGATTAACATATCTTCTTTGACCTCCAGTTACACGAAACCGGTTCGCATCGGAGCGAGTCCACTGACATCTAAGACGCTTTTCGGCctcttacaacttttcatatatttcaatttttttaccaattgtgttatattatcataattttgaGTGCTAAACTCCCcttgaaactgtaaaatttgatgtcgctccgatatcgtgtaactggggccttatATTTCTAATACGACAAATTTGTGATACACCTAGGAGGTTGACGGAATGAACCTTAAATAAAGGCTATCGCTAGCTGTTTCGCTGGTTTTCACATTTCACATTTTCACACAAAAATCAGCTCTTTTAATCACCCACATAAATGGCACTTGAACAGTGGTTTCCTATATGCGGGTTTTTAACTGGTATTCTAGTGTATATTTTGTTGGAAATATTCGTAAATAATATACAGTCTTGAAATACTATACCTTATATTATGTAGAATTAGTTACAGAACTGTATAAAAACGCATACGATTGACATTATGTTTGTTTCAGAAAATATTATTTAGCTATATTATTAATATCGTatagttttgtttttaatttgtatgtatatatagtagacgtgattaaatttattaaagGACTATTTAATTCGTCAACAATAGACgttttggcattttttgttCGCGCGTTTGACCATATTGAAACAATACGCCTTATagtgtaaaaatattttcggtCTTCAAAAACGCCAACAAAAACAGCAACAACGGTGGTTTTATAAACGGAAGTTTGACATTAAGCAGGGGAATGCGATAATTTAGTGAGATAACTATTTGTTTTGTCAGCGTCAGCAAGTTAGTAGCAACCCAATATACTGAAAAATTAGATGCTATCGCGATCCTAACTCGACCCTCTATAGGCAATGCAATAAGTTTAGCTAGGTTATTAAAACACGCGGGCTACATATGAACGAACAGCATTCGAAGTTTACCGGTTGTTCAATTTCGACAAGTCCATGCTCATTGCGAATGTTATGTCTATATTTAAATACGAATCCCGTGACTATCACCGCTAAGAACAAAT

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)	OG0007630 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14719 all species →	PID_2	Phosphotyrosine interaction domain (PTB/PID)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR006020 all species →	Domain	PTB/PI domain	Interproscan
IPR051133 all species →	Family	Adapter and Engulfment Domain-Containing Protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11232 all species →	PHOSPHOTYROSINE INTERACTION DOMAIN-CONTAINING FAMILY MEMBER	Interproscan

Gene Ontology

No Gene Ontology signature was detected for CAB4004575.1. This gene does have a gene model — the search simply returned no hit.

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
K12474	LDLRAP1, ARH; low density lipoprotein receptor adapter protein 1	-	Membrane trafficking	ko04131	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4004575.1 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

21TPM > 0

4Conditions

806.5Max TPM

78.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	20.84	37.97
apical branchlet · Temperature treatment at T0	6	6	24.98	51.71
apical branchlet · Temperature treatment at T25	5	5	245.45	806.46
apical branchlet · Control at T0	4	4	34.29	50.18

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	37.97
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	27.59
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	24.04
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	15.43
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.32
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.71
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	51.71
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	30.61
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	26.13
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	19.75
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.48
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.19
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	806.46
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	134.42
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	111.28
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	89.06
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	86.04
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	50.18
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	34.23
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	27.56
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	25.21

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.