Gene detail

Detailed information of CAB4000328.1 in Paramuricea clavata

Genomic Location: pcla8_s003881:14461...17057
NR annotation: CAB4000328.1, E3 ubiquitin- ligase SIAH1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A013627

CAACTTCGTCACGGTTCAAGTGTTGATCGATATTTTGGAAGAGAAAACATCAGTGCGATATTAGTTCACAGAACCGAAATTTAATGGGATCTTCAAGCCGTTTGAAGGCAAATGAAAAGATGCTGAAGCACAAGGATTGCTGTACGAGAATGGCAAGGTCCTAAAACGTGCGCAAAACGCTGAACAAACAGCGATACGGCGCCTGTATTTGTGGAGTTTAAGAAAGGCAATTATGTCCATGAATCGACCATCAGCTGCCGCTTCAGTTAACAGAAAGATGATTCGACAAAATCCGTCCGCTTCTCAGGCAGTCGCGAGTGCCAACGTAGACCTTACAAGTATTTTTGAATGCCCTGTTTGCTTTGACTATGTCTTACCGCCGATTCTACAGTGTTCTAGCGGCCATTTGGTTTGTTCAACTTGTCGCCCTAAACTACAATGTTGTCCGACATGTCGTGGGCCGCTTGGCAGCATACGAAATTTGGCAATGGAGAAGGTCGCCAGCACGATAATGTTTCCTTGTAGATATAACTCTGGGGGTTGTGGGGTCTCCCTGCCTTTTTCAGAAAAGACGGAACACGAAGAATCCTGCGAGTTCAGACCGTACACCTGCCCCTGTCCGGGGGCTTCTTGTAAGTGGCAAGGGGCTTTAGATGCTGTAATGCCCCACCTTATGCACACACACAAGTCCATCACTACCCTTCAAGGCGAAGATATTGTATTTTTAGCGACGGACATTAATCTCCCTGGCGCGGTCGACTGGGTTATGATGCAGTCCTGTTTCGGGCACCATTTTATGCTCGTCttagaaaaacaagaaaaattcGAGGGCCATCAGCAGTTTTTCGCCATTGTTCAACTCATCGGCACACGAAAACAGTCGGAGAATTTCGTCTATCGGTTGGAGCTTAATGGTAACCGTCGACGACTCGCATGGGAAGCCACGCCCCGTAGCATTCATGAGGGAATCTCGTCCGCGATATCCAACAGCGATTGTCTGATTTTCGATACAAGCATGGCGCAATTGTTTGCCGAGAATGGTAACTTAGGTATCAATGTCACCATTTCTATGTGTTGAAGCCGGATGCTTACCAGTTGAAAGTGGTAAAGTTCACTAATCGAGATATGTTGACGGATGTTGGCCATTGAGCGAAATGCGTGTACAGTCAAAATGAATGTTCAGCGATGCTTACGAATATTGAAAGAAGTTCAATATGCTAACTGAATGTCAAAGAACACTTAGTCGTCAAGAGAATTGCTCTGACGAGACGTTATATGAAGTACTCTTTGTGGTGTATTGTTGGAATGTCAAAGGCTCAAGGAGCCCCATATTTTGAAATAGGAGAGAAACATATGCTGAAATGTAGTGTAAGATCTGAAGGTAGCATCGGTTATCGTAGGCCGGACGAAGTTAATTTGACGTACAAATTTTAGGTCAAGAACACATTTAAATACTCTGGAAAAATACTCTGGTTCTGAACGAATAATAGTATATTGAACAAACTTGAaaaagtttattaattaattaattaagcattATTCTACGAGAAAGTTTCTTTATAACAAAGcaacaaattaaaattgttgCCCTGGTTTGTAACTGAATCAACTAAGAAAGATGGCTACCAGGCCGTCTCGAATGTCAAAGCGTTTTCGATCTGGACACTAACAATGGCAGCTTATAGACCTTTATCAGAAAAATTTGGTGGCTTTTGGCTTAAAAACTGTGGCATTGGtgctattttttaaaaacattttattagaAAATATACATAGGTAAATATAAGCAGAACGTCAACGTCTACAGACTTTCTGAAGAGACCTTGGCTCAAagtgccacagtttttaaaatatagcCTTCAAATTTTTTCTACATACTAATTTTGACAGTGCCATTATAACCGAGGCAGCAAATGAAATTGATCTGGTCTTAGCTTTATTTGAAGTTAcatcaaaagtcaaaacaatgCCGTAATTATACTTCGAACGCGATACTAGCCGTGTCAAGCTGAGCTGTTACCAATAACGTCTAAACACACATTGGTTTTAAAATATCTGGGCAGTTTTTGTCAAGACTATCATAAACTACTCCGAGTTTGACCTATAAAATTTAACTCCATCTTACAGAGAAAAATGTATGTATTATACAAAATAAGCTGATATGCAAATAGATGGCATagtaaaaatattgtaaaaaggtattggttgaaaaatataaaaactttatgagttttattgttttatttgcTCTTCATTTTAGCTTGAAGCTGCTTTTTATTAGATTACAATTACATTTACAGCGCCTGGTCAAATCTTATATATTTGCTTTTGCAACAAAGCCTACAAAATGGGCATCCCTATGACGTAGATATATTGCTGTATCCTAATCTGGTCATTTGAAAGGCGCTACTGTATGCAATGAAGGTACCGTAGTTAACCAAATAACCAATTGAGACTCTcccttttgaagagtaaaatcatctggtgttagaccgAGTAAAATCCAGCATTAGTTTctctttttaattaattaaggtaTTTTCCCTTTTAAGAAAATTTTGGCAACTAGGAAATACATGtatgaaggaaattttgaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P61092	E3 ubiquitin-protein ligase SIAH1A OS=Mus musculus OX=10090 GN=Siah1a PE=1 SV=1
Q920M9	E3 ubiquitin-protein ligase SIAH1 OS=Rattus norvegicus OX=10116 GN=Siah1 PE=1 SV=2
Q8IUQ4	E3 ubiquitin-protein ligase SIAH1 OS=Homo sapiens OX=9606 GN=SIAH1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007542 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21362 all species →	Sina_RING	E3 ubiquitin-protein ligase sina/sinah, RING finger	Domain	Interproscan
PF03145 all species →	Sina_TRAF	Sina, TRAF-like domain	Domain	Interproscan
PF21361 all species →	Sina_ZnF	Sina, zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR049548 all species →	Domain	E3 ubiquitin-protein ligase Sina-like, RING finger	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR018121 all species →	Domain	Seven-in-absentia protein, TRAF-like domain	Interproscan
IPR013010 all species →	Domain	Zinc finger, SIAH-type	Interproscan
IPR008974 all species →	Homologous_superfamily	TRAF-like	Interproscan
IPR004162 all species →	Family	E3 ubiquitin-protein ligase SINA-like, animal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45877 all species →	E3 UBIQUITIN-PROTEIN LIGASE SIAH2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0007275 all species →	Biological Process	multicellular organism development	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0031624 all species →	Molecular Function	ubiquitin conjugating enzyme binding	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K04506	SIAH1; E3 ubiquitin-protein ligase SIAH1	EC:2.3.2.27	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 CAB4000328.1 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

19TPM > 0

4Conditions

42.4Max TPM

16.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	21.82	32.34
apical branchlet · Temperature treatment at T0	6	5	14.57	42.39
apical branchlet · Temperature treatment at T25	5	5	18.78	38.85
apical branchlet · Control at T0	4	3	7.12	13.87

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	32.34
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	30.96
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	20.77
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	18.59
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	14.65
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	13.62
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	42.39
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	28.23
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.34
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.20
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.27
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	38.85
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	25.53
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	12.80
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	10.28
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	6.42
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	13.87
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	10.51
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	4.12
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.