Gene detail

Detailed information of CAB3983507.1 in Paramuricea clavata

Genomic Location: pcla8_s000647:26387...29637
NR annotation: CAB3983507.1, Hypothetical predicted protein [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A016230

ATGGATGACGCTGTCATCTGTGGACAACTCAGGCAAATTTTTCCGCAAATAGAGCTTAATGTTATTCAAAGAACCGTCGAAGAAGCGAAGACAAACGAAGGAGTCGACATTTTGACACATTGCATTGAGGTTGTTCTCGCTCGTCAAGAAGAAGCAAGGTGGTTTGGGAACAACAATAATGGGCAACAAGGAAACGACGATGTTGTTGTTGTTAAATCCATTAGGAAGGAAACTTCAAGGAAAGGAAAAACGAGAGATATTCCTGTAGTTTTAGTCAGAGAAGATGGGCCTGGTCAATTGATTCGCCCCCAACGAGAAACACCTCAGCCGTTCTCAGATATCGACTCGGACAATTATCCTGGATTCGAAAGTAGTGACGACGAAACTGATGATCCAATAAGATACATGAATAAATTCAATTACAATGGGGACAGTAGTCCAATAGGAGATCAATTCTCTGATGACAATTTTGATAGGTTAATCACAGACTTGTCGTCCCCACCTTTAGCTATTGTCCCTCAACAAATGACAGCACCAGCTAGTCCATTGAGATCTACAGTGATAAAACATTTGACTTTTGACGAACAACAACACCAGCAACCATCAACCACCCCTAATCGGCAACCTTTGGCAACACCCGGTCAACAACCTTCAGAAACTCCCATCAGGCAACTTCCAGCAACACCCGTCATGCAACTTTCAGCAACACCTATCATGCAACCTTCTGCAACACCCATTTGGCAACCTTTAGCAATGCCAATAGAAAAACCATTAGTAACTCCCAATCAACAAAGTATGCCAATGGGATGCTCACTACTTGATTTCATTAAACAAATGTTCCCGAAAGTAAACAGACAGTTTGTTCAAAATCTATCCCAACAGGGTCATGATCTAAACAGTATTGTAAACATACTTATTGATCGACCTGACATGCAAAAGTCTGACTCAAGTTCGAATCCACCATCTCCTAAAGAACCAGCACAAACCAAAGAGATTGATTACTTCACAGACTTTTCTCAAAAAGTATCACCTTTGTACCATCGCCCATGTGAATATCTGCTACGGAATGAGTTTCAACGAGTTTCAGTAGTCGACATCAGAAAAGCAATGCAAATATGCAATGACCACTATGCCCCGGCCCGGAAATTACTTGAAGAAGCACTTGTGGAGATGAACCAGAATCGAAGAGGTAAATCACCACAGGCAAGTACATTGCCAAAAGGCAGTGCAGTGCCACAGAGCAGTACATCACTACAGAGCAGCAGCTTGCCAACCACCTCTAATTTAACACGGAAAAATAAATTTACCATAACCCGGTTATTGGCAAGCAAACGAACACCAGTGAAACTTTTTGACAAAATCCATCCTGAATTGCAGCTAGAAATAGATTTTGTCAAAAAACGGAAAATGTTAAATGAAGAGAAGAAGAATGCCATCTATGCTGCACATGTTAATAAGCAACAGTACATAGATGAAGGAGAACTAATTGAATGTGGTTGTTGTTTTGGAGAATTTCCATTTGAGGAAATCATTCAGTGTAGTGATGGCCATCTTTTTTGTAAAGAGTGTCTCCATGGTTATGCAAAGGAGATCATATTTGGTTCAGCTATGACATCTGTGAAGTTAATTTGCATGGGAGAGAGTTGTGATCAACCATTTCCATACAATCAATTGGAAAAGTGTCTGACAAAGAATGAAATTGAAAAATACCAAGGCAGACTTCAAGAGGATTGTTTAGCCAAAGCTGATATTCCAAATCTCCACCAATGCCCATTTTGTGAGTTTGTTGCCATTATACCAGAAACAGAGAAGGTGTTCACCTGCATGAATCCAAAATGCATGAAGGAAACATGTATAGAATGTAATGAAGAATGGAAGGATCATTTTGGGAAAAAATGTAATGAGATTGAAAAGAAATCTCAAACGAACCTAAGACTGAGTTACGAAGAAAGAATGACCGTGGCAAAAGTGCGGAAATGTGCAAAGTGCTCATTGACTTTCACAAAGCAAGACGGTTGTAACAAGATGACATGTAGATGTGGTACTACTCAATGTTATGTTTGTCGTAAATCATCAATCAATTATAATCATTTTTGCCGACATCCTCGAGATCCTGGTAAGAAGTGCCAAAAATGTACAGCATGTTCTCTGTGGACAGATCCAACTGAGGATGATGACTTAGCAATCAAGCAGCTTCAGGAAGAATCAGTAGTGGCCAAGAGGAAGCTTATGGAAGAGATTGAACAGTCTGCCAGTAAGAAACAAAAAGTTTAA

Transcript

rna-PACLA_8A016230

TCAAACTTCATTTTGTTCCAAATCCTGCAATATGATTGGCCAATGTTAAAGGCCCACTGTGAAATCTGAAATGATACGACATTGACACACATTGATTCATACTTTCTGGTCGACAGTCAACTCACATTGTTTTTTATACAGTGTTTAAGGAAGCAATTTAActatttatacaatataaatgttagCCAATGGATGACGCTGTCATCTGTGGACAACTCAGGCAAATTTTTCCGCAAATAGAGCTTAATGTTATTCAAAGAACCGTCGAAGAAGCGAAGACAAACGAAGGAGTCGACATTTTGACACATTGCATTGAGGTTGTTCTCGCTCGTCAAGAAGAAGCAAGGTGGTTTGGGAACAACAATAATGGGCAACAAGGAAACGacgatgttgttgttgttaaatCCATTAGGAAGGAAACTTCAAGGAAAGGAAAAACGAGAGATATTCCTGTAGTTTTAGTCAGAGAAGATGGGCCTGGTCAATTGATTCGCCCCCAACGAGAAACACCTCAGCCGTTCTCAGATATCGACTCGGACAATTATCCTGGATTCGAAAGTAGTGACGACGAAACTGATGATCCAATAAGATACATGAATAAATTCAATTACAATGGGGACAGTAGTCCAATAGGAGATCAATTCTCTGATGACAATTTTGATAGGTTAATCACAGACTTGTCGTCCCCACCTTTAGCTATTGTCCCTCAACAAATGACAGCACCAGCTAGTCCATTGAGATCTACAGTGATAAAACATTTGACTTTTGACGAACAACAACACCAGCAACCATCAACCACCCCTAATCGGCAACCTTTGGCAACACCCGGTCAACAACCTTCAGAAACTCCCATCAGGCAACTTCCAGCAACACCCGTCATGCAACTTTCAGCAACACCTATCATGCAACCTTCTGCAACACCCATTTGGCAACCTTTAGCAATGCCAATAGAAAAACCATTAGTAACTCCCAATCAACAAAGTATGCCAATGGGATGCTCACTACTTGATTTCATTAAACAAATGTTCCCGAAAGTAAACAGACAGTTTGTTCAAAATCTATCCCAACAGGGTCATGATCTAAACAGTATTGTAAACATACTTATTGATCGACCTGACATGCAAAAGTCTGACTCAAGTTCGAATCCACCATCTCCTAAAGAACCAGCACAAACCAAAGAGATTGATTACTTCACAGACTTTTCTCAAAAAGTATCACCTTTGTACCATCGCCCATGTGAATATCTGCTACGGAATGAGTTTCAACGAGTTTCAGTAGTCGACATCAGAAAAGCAATGCAAATATGCAATGACCACTATGCCCCGGCCCGGAAATTACTTGAAGAAGCACTTGTGGAGATGAACCAGAATCGAAGAGGTAAATCACCACAGGCAAGTACATTGCCAAAAGGCAGTGCAGTGCCACAGAGCAGTACATCACTACAGAGCAGCAGCTTGCCAACCACCTCTAATTTAACACGGAAAAATAAATTTACCATAACCCGGTTATTGGCAAGCAAACGAACACCAGTGAAACTTTTTGACAAAATCCATCCTGAATTGCAGCTAGAAATAGATTTTGTCAAAAAACGGAAAATGTTAAATGAAGAGAAGAAGAATGCCATCTATGCTGCACATGTTAATAAGCAACAGTACATAGATGAAGGAGAACTAATTGAATGTGGTTGTTGTTTTGGAGAATTTCCATTTGAGGAAATCATTCAGTGTAGTGATGGCCATCTTTTTTGTAAAGAGTGTCTCCATGGTTATGCAAAGGAGATCATATTTGGTTCAGCTATGACATCTGTGAAGTTAATTTGCATGGGAGAGAGTTGTGATCAACCATTTCCATACAATCAATTGGAAAAGTGTCTGACAAagaatgaaattgaaaaatacCAAGGCAGACTTCAAGAGGATTGTTTAGCCAAAGCTGATATTCCAAATCTCCACCAATGCCCATTTTGTGAGTTTGTTGCCATTATACCAGAAACAGAGAAGGTGTTCACCTGCATGAATCCAAAATGCATGAAGGAAACATGTATAGAATGTAATGAAGAATGGAAGGATCATTTTGGGAAAAAATGTAATGAGATTGAAAAGAAATCTCAAACGAACCTAAGACTGAGTTACGAAGAAAGAATGACCGTGGCAAAAGTGCGGAAATGTGCAAAGTGCTCATTGACTTTCACAAAGCAAGACGGTTGTAACAAGATGACATGTAGATGTGGTACTACTCAATGTTATGTTTGTCGTAAATCATCAATCAATTATAATCATTTTTGCCGACATCCTCGAGATCCTGGTAAGAAGTGCCAAAAATGTACAGCATGTTCTCTGTGGACAGATCCAACTGAGGATGATGACTTAGCAATCAAGCAGCTTCAGGAAGAATCAGTAGTGGCCAAGAGGAAGCTTATGGAAGAGATTGAACAGTCTGCCAGTAAGAAACAAAAAGTTTAAGCATACGTTGTGTTTATTTTAGAAATACTGTTTGCCAAAGAAATTCTTGAAGTTGCATAATATTACAGTATCTCTTGTCAGGATAAATTAAGATGCATGTGCATTTAAGTTTATACTAAGTCAAAAGTTcttgaccaaatttttttacATAGCCACAAATTCTTTTGCACTTGGTTTTCTCACAACCTGGCCAAGTGAATACACCCTgtcaataattacgtcatttggccttggagcctcgctctcatgaatcgtaaGACAATCACATTgcataatttactaatgagagcgaggctccaagaccaaaaaatatgacgtaattattgaaagggtgtattgcaCATGCACCTTTAGACAGAATCTGCTTTTTAATAGTGGAGTAATACTATTTTTTCCATAAGTATTCCAAGATATCTATAAAATGGTTACAAAAGTAGAATATTTAATTCATATTTGGAGTTAGTCTTCAACATGAAACAGATGAACTaaagaattcaatatatttatatagagaCAAAGATTGACAATAGACAATCTATATAAATTGCAAATAATGTAATTTTTGTTGGGGAATTGTTTTGTTAGAAataagaattttttcttcagaaatatataaattattctgGATTATGTGGTGTGGTGATAATCCATAAAGTTAATTGTTCTGATTGTAGCTGGTTAATCCAATCTTGGTTTTATAGATTCGATTAGCCACAAATCTCACAATTATTTGCATGGGTTTGATTACCTCACAGGCGTTTGTTGTGGGTGATTTCAATAAACTTGGCA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9NWF9	E3 ubiquitin-protein ligase RNF216 OS=Homo sapiens OX=9606 GN=RNF216 PE=1 SV=3
P58283	E3 ubiquitin-protein ligase RNF216 OS=Mus musculus OX=10090 GN=Rnf216 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007151 (this species only)
Ubiquitin family	E3\|E3 activity\|RBR · all ubiquitin genes in this species

Pfam domain

No Pfam domain signature was detected for CAB3983507.1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR047544 all species →	Domain	E3 ubiquitin-protein ligase RNF216, RING finger, HC subclass	Interproscan
IPR047545 all species →	Domain	E3 ubiquitin-protein ligase RNF216, BRcat domain	Interproscan
IPR051628 all species →	Family	Linear Ubiquitination-Associated E3 Ligases	Interproscan
IPR002867 all species →	Domain	IBR domain	Interproscan
IPR047546 all species →	Domain	E3 ubiquitin-protein ligase RNF216, Rcat domain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR044066 all species →	Domain	TRIAD supradomain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22770 all species →	UBIQUITIN CONJUGATING ENZYME 7 INTERACTING PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin binding	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0071797 all species →	Cellular Component	LUBAC complex	Interproscan
GO:0097039 all species →	Biological Process	protein linear polyubiquitination	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	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
K11976	RNF216, TRIAD3; E3 ubiquitin-protein ligase RNF216	EC:2.3.2.31	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 CAB3983507.1 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

18TPM > 0

4Conditions

77.4Max TPM

13.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	21.49	77.42
apical branchlet · Temperature treatment at T0	6	6	16.40	38.39
apical branchlet · Temperature treatment at T25	5	4	6.38	17.98
apical branchlet · Control at T0	4	2	3.99	12.97

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	77.42
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	18.44
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.10
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	10.00
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	6.50
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.50
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	38.39
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	37.83
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.27
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.81
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.23
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.88
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	17.98
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	7.01
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	5.18
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.72
SRR19977434	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	12.97
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	3.01
SRR19977442	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.