Gene detail

Detailed information of CAB3977789.1 in Paramuricea clavata

Genomic Location: pcla8_s000082:6237...9199
NR annotation: CAB3977789.1, E3 ubiquitin- ligase HECTD3-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A056722

ATGACAAAAGACCACGCTAGGAAGCGTCTAGCACGGATCAGATGTGTTTTTGAGTGTGTAGAATCAATACGAGACGGGAAAGAGCTACCAGACGCGTTGTGTTTTGTTCCCGGTAGTGTGAACTACAAATTTCAAAGTGAAAGGACAACCTCAATTGTAATTAGAGATTCCCCATCTTCTTCCTCAGCAAAAATTGGTGAAATTCCTTACAAAGTAAGTACAAGATTTACCGCTAGCGGCGAGGAATACTGGAACGATGAGGGTCTATGGCTAAGACTTGTGCCTGAAAGTTTAAAGAAATTTGACGTGGACAGCAATCACTCAGCAGGGTGGGTGTTTATTCATTCCCGTGATAATAAAGTTAAAGACGAAGTTGATTTAGCGACAGTGAATTCCAAGAAAAAAAGCACGAAGCCTGTTCTAATGAACTGGGAATATGCAGTTGATACCTACTACTCGCTTAAAATTTCACAGAATGCAGAAACTTTACATGGGCAAGCCGACCTTGAGGCCATGAACAAATTAAAATTCCCCCCTCAAAATTGGAGCCTGGAAGCTGATGAAGAATTGGCTCGTTTCATTAGTCAGAATGTTACCATTCAGAAGGAGGCAACGTTGGGCAATCTAAGTCAGTATGTCGAATCAATTGAAGTGTCATCCCAAAGTCAATATATTTCAGCATTGACAGATGGAGACATTGAGACATATTGGGAATCTGATGGATCTCAAGGTCAACATTGGATACGTCTTAAGATGAAACCCGGGACAGTAATCAAGCAATTGTTTGTAAACGTGAATAGTAATGATGATAACTACATGCCAAATCGATTTCAAGTACATGGCGGAGAAACTGGTAATGTGAAGTTGCTGAATGACGTCGCAATAGATTCAAGTAAAACTGGTGATGTTCTAATACTCGAAGATATGACCCAACATTGTCCTATTATTCAAATTTGGATTAAGGACTGCAAAGATGATGGAATTGATACCCGCATCCATGGAATCAAGATTGTTTCAACTGATGAGAAAGAACCTGGTTTGAGTGCAGACACTTTCAAGAATAAGACAAAGATTATCCGTTTCCCGAAGTTAGAACATGTTAATCCTGACCTACTTTACAATAGAGCAAGAAGTTTGTTGAGATTTGTTGCTCTGTTAGATAGTGTCCTTCCTTTCATCTTTCCAATTTGGAAGTTTACGATTGGCTCTTACACAAGTCTGGAACTGATTAGGCAGTTGCTTCCTCTTTCACGTCGTAGGATTACATTGATTGATCAACTTATCCTTGAATCACAGTCATGTATTACACTTCCAAGTATCCCAAAGGTTGTTCTGAACCGTCATACCGCTGCAGAACATCGGGAGAACCCTGCAAGTGATCCAGAAGGAAAGCAATCAATTTTTTGTCAGTTATATGAAGCATTGAAGTCAGAGAAATGTGGGGTGACACTTGATTTCCGTTGGTCAAATCGCTATGAACAGTGGTGGGAATGCAAGTTTATCTCGGAAGGTATTATTGATCAAGGTGGTGGCTTTCGTGATTCTCTATGTGACCTTGCTGAAGAAGTATGCCCTAGTTCTGCAGATTCATTGTTGCCATTGCCTTTATTTATCCGTAGTCCTAACCAGCTGTACGATTCATCTAATGTTTATCGTGATGGTTACATTCCAAACCCATCCTGTCGATTATTTGACCAATATGAATGGCTTGGAATGCTGATGGGTGGCCACCTGCGTGGAAGAGAGAGCTTACTGTTATCATTTCCTAAGTTTATATGGAAACAGTTGCTTGGTGAGAAAGTTTCATGGCTAGAAGATTTTGTCACAGTTGATGCAGCATTGGTGAAGCTGGTTGAATCCATTAAGCAAATGGATCGGAAGAAATTTGAAGAGAAGTTTACTGATATTCTTACTTACACAGCAGTTTTAAGCAATGGCACAATTGTTCCTCTCATTTCAAATGGTGAAGATGAAGTTGTCAAATATGAAAACCGTGTTGAGTATACTGAGCTGCTTCAAACTGCAAGAATGCATGAAAGTGAAGAGCAAGTCAATGCCATCCGTCATGGTTTAGCTAAAGTGGTTCCAGTGTCGTTGCTTGGACTTCTCACATGGCAAGAACTTGAACTAAAGGTCTGTGGAAATCCAAAGGTGAATGTTGAAGATCTTCGCAAGACAACTTATAGTGAGGACTTGCCTAAGACAGATGAGAGAGTAAAATATTTTTGGAAAGCCATGGAAAATTTCAGCAATGATGATCGAAGTCGATTTTTGAGATTTGTGACTGGCAGGCGTAGATTACCCGCAAACATGACATTGTGTGCTGCAAAAACAACTGCACCTGTTGATTCATTACCTGAGGCTGCAACTTGTTCAGGTACTTTATTTCTTCCTTGTTATTCTTCTTATACTGCAGCTGAGGAGAAATTGCGTTATGCAGCATACAATTGTGTATCCATTGACACTGATGGCTCATGGGATGAGTGA

Transcript

rna-PACLA_8A056722

GGCCGAGCTCCGATGACGAAATTGGCGGAAATTGCTAGAATTAAAGCATAAATGGTGTGTTTACGtggaaaaagtacaaattttgccATGATTTTGAGTTAAAAATGACAAAAGACCACGCTAGGAAGCGTCTAGCACGGATCAGATGTGTTTTTGAGTGTGTAGAATCAATACGAGACGGGAAAGAGCTACCAGACGCGTTGTGTTTTGTTCCCGGTAGTGTGAACTACAAATTTCAAAGTGAAAGGACAACCTCAATTGTAATTAGAGATTCCCCATCTTCTTCCTCAGCAAAAATTGGTGAAATTCCTTACAAAGTAAGTACAAGATTTACCGCTAGCGGCGAGGAATACTGGAACGATGAGGGTCTATGGCTAAGACTTGTGCCTGAAAGTTTAAAGAAATTTGACGTGGACAGCAATCACTCAGCAGGGTGGGTGTTTATTCATTCCCGTGATAATAAAGTTAAAGACGAAGTTGATTTAGCGACAGTGAATTCCAAGAAAAAAAGCACGAAGCCTGTTCTAATGAACTGGGAATATGCAGTTGATACCTACTACTCGCTTAAAATTTCACAGAATGCAGAAACTTTACATGGGCAAGCCGACCTTGAGGccatgaacaaattaaaattcCCCCCTCAAAATTGGAGCCTGGAAGCTGATGAAGAATTGGCTCGTTTCATTAGTCAGAATGTTACCATTCAGAAGGAGGCAACGTTGGGCAATCTAAGTCAGTATGTCGAATCAATTGAAGTGTCATCCCAAAGTCAATATATTTCAGCATTGACAGATGGAGACATTGAGACATATTGGGAATCTGATGGATCTCAAGGTCAACATTGGATACGTCTTAAGATGAAACCCGGGACAGTAATCAAGCAATTGTTTGTAAACGTGAATAGTAATGATGATAACTACATGCCAAATCGATTTCAAGTACATGGCGGAGAAACTGGTAATGTGAAGTTGCTGAATGACGTCGCAATAGATTCAAGTAAAACTGGTGATGTTCTAATACTCGAAGATATGACCCAACATTGTCCTATTATTCAAATTTGGATTAAGGACTGCAAAGATGATGGAATTGATACCCGCATCCATGGAATCAAGATTGTTTCAACTGATGAGAAAGAACCTGGTTTGAGTGCAGACACTTTCAAGAATAAGACAAAGATTATCCGTTTCCCGAAGTTAGAACATGTTAATCCTGACCTACTTTACAATAGAGCAAGAAGTTTGTTGAGATTTGTTGCTCTGTTAGATAGTGTCCTTCCTTTCATCTTTCCAATTTGGAAGTTTACGATTGGCTCTTACACAAGTCTGGAACTGATTAGGCAGTTGCTTCCTCTTTCACGTCGTAGGATTACATTGATTGATCAACTTATCCTTGAATCACAGTCATGTATTACACTTCCaagtatcccaaaggttgtTCTGAACCGTCATACCGCTGCAGAACATCGGGAGAACCCTGCAAGTGATCCAGAAGGAAAGCAATCAATTTTTTGTCAGTTATATGAAGCATTGAAGTCAGAGAAATGTGGGGTGACACTTGATTTCCGTTGGTCAAATCGCTATGAACAGTGGTGGGAATGCAAGTTTATCTCGGAAGGTATTATTGATCAAGGTGGTGGCTTTCGTGATTCTCTATGTGACCTTGCTGAAGAAGTATGCCCTAGTTCTGCAGATTCATTGTTGCCATTGCCTTTATTTATCCGTAGTCCTAACCAGCTGTACGATTCATCTAATGTTTATCGTGATGGTTACATTCCAAACCCATCCTGTCGATTATTTGACCAATATGAATGGCTTGGAATGCTGATGGGTGGCCACCTGCGTGGAAGAGAGAGCTTACTGTTATCATTTCCTAAGTTTATATGGAAACAGTTGCTTGGTGAGAAAGTTTCATGGCTAGAAGATTTTGTCACAGTTGATGCAGCATTGGTGAAGCTGGTTGAATCCATTAAGCAAATGGATCGGAAGAAATTTGAAGAGAAGTTTACTGATATTCTTACTTACACAGCAGTTTTAAGCAATGGCACAATTGTTCCTCTCATTTCAAATGGTGAAGATGAAGTTGTCAAATATGAAAACCGTGTTGAGTATACTGAGCTGCTTCAAACTGCAAGAATGCATGAAAGTGAAGAGCAAGTCAATGCCATCCGTCATGGTTTAGCTAAAGTGGTTCCAGTGTCGTTGCTTGGACTTCTCACATGGCAAGAACTTGAACTAAAGGTCTGTGGAAATCCAAAGGTGAATGTTGAAGATCTTCGCAAGACAACTTATAGTGAGGACTTGCCTAAGACAGATgagagagtaaaatatttttggaaagCCATGGAAAATTTCAGCAATGATGATCGAAGTCGATTTTTGAGATTTGTGACTGGCAGGCGTAGATTACCCGCAAACATGACATTGTGTgctgcaaaaacaactgcaccTGTTGATTCATTACCTGAGGCTGCAACTTGTTCAGGTACTTTATTTCTTCCTTGTTATTCTTCTTATACTGCAGCTGAGGAGAAATTGCGTTATGCAGCATACAATTGTGTATCCATTGACACTGATGGCTCATGGGATGAGTGATATGTTATAGAAACTTTCTAAATAAAGTAGTTTTGTATGAAATTGATAGTTTTAAGTTatcaacattgaaataacaaAGTAATAAGCAATTTATTCCTTAGGAAATAATCTGCATGACTGAATACACTGCTTGAGTGACAATAAATTGTTTTTATGTAAGATTTAGTGATGATGTTGGATATATGACCGTGGaagtgaatattttaatacacatTAATTTTTATACTCTAAAGTTTACTGTAAGTGTTACCTAGGTTTTGcatgaaaaatgtttttgtcAACCACCTAATAATATAATTCTGATTGGCTGCCTATAAACAGTGCAATTTTATTCAAATACCAAATTGGTGGATTTCTAACCTGGAAAGTACG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5T447	E3 ubiquitin-protein ligase HECTD3 OS=Homo sapiens OX=9606 GN=HECTD3 PE=1 SV=1
Q3U487	E3 ubiquitin-protein ligase HECTD3 OS=Mus musculus OX=10090 GN=Hectd3 PE=1 SV=2
Q15751	Probable E3 ubiquitin-protein ligase HERC1 OS=Homo sapiens OX=9606 GN=HERC1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001728 (this species only)
Ubiquitin family	E3\|E3 activity\|HECT · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00632 all species →	HECT	HECT-domain (ubiquitin-transferase)	Domain	Interproscan
PF03256 all species →	ANAPC10	Anaphase-promoting complex, subunit 10 (APC10)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004939 all species →	Domain	APC10/DOC domain	Interproscan
IPR000569 all species →	Domain	HECT domain	Interproscan
IPR042469 all species →	Family	E3 ubiquitin-protein ligase HECTD3	Interproscan
IPR035983 all species →	Homologous_superfamily	HECT, E3 ligase catalytic domain	Interproscan
IPR008979 all species →	Homologous_superfamily	Galactose-binding-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46654 all species →	E3 UBIQUITIN-PROTEIN LIGASE HECTD3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	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
K12233	HECTD3; E3 ubiquitin-protein ligase HECTD3	EC:2.3.2.26	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3977789.1 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

17TPM > 0

4Conditions

48.2Max TPM

12.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	11.13	38.64
apical branchlet · Temperature treatment at T0	6	6	17.02	48.24
apical branchlet · Temperature treatment at T25	5	5	14.38	33.37
apical branchlet · Control at T0	4	2	4.81	15.63

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	38.64
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	10.61
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	9.62
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	7.93
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	48.24
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	16.58
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	13.43
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.98
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.70
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.20
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	33.37
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	19.11
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.89
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.70
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.84
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	15.63
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	3.61
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
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.