Gene detail

Detailed information of CAB3981815.1 in Paramuricea clavata

Genomic Location: pcla8_s000453:72353...76847
NR annotation: CAB3981815.1, Hypothetical predicted protein [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A021280

GCGGTTTTCAATATGGCGCCCAAATCTGACGTTTAATTTCAAGGTATGTTTTGCAATTGTTTTTCATCGTTTTAAAGAACATAATGGCAATTTTCGTCGGGTTTTCGCGACGGTACTGAAAGGGTTGCTTATGTATAGTATGCTAAAGCCTGAAAGGGATtgattatatatttgtataaaacaAGTAGAATGTTTGAATGAACTTGTATGTCGGGCTGTGAGCAGGCTGTCAGGTGGTAACTTGTACGTGCAATTGTGGATCTATGCTAGTCTATAGACTTGCAAAACTAGTACATTTTGGTCACGCAACACGgatgttttaataattttgtacttTTCTTGATTTGTTTGCAATGAAAACATTGCTTTGGCAACATATTTGATACttcttttaatataatttatatatagacACTTGTAGTGTTccactacccccccccccctgacagTTAATAGACAGTTAAATAGAAAAGTAGGGCATATTGGCACTTAACCATTGAGTGACAGTAGTCtcccccttgacaagtaaaattgtctggcgttagacagagtagaataatatgatgttagacagaataaaataataaaatacggCACATCTGGGCTAATGGGGTCCATGGGCAGATAgactgattaacccattgagtggcagcactctctccttgatgagtaaaatcgcctggcattagacagagtaaaataataaagtagggcgcattgccacttaaagggttaaattaactttaattAACACAACATTTTCTTGGCTTCAACTGTGATAGGCAACAAAATGCTACATAAAAGGAGACTCAAAAGCTACAAACTTATAAAGCATTAACATTTATGCATGTTGGAGGTTTCACACAAGGTTTTAAAAATTGGCTGTAGTTTGATACACTTATTTCAAATATCAATCtttcaatattaaaaaaaaatgttcacaatattacacaaaaacatcaaaattacATAAAAAAAACCATAAAAATTTTCCAAGATTTTTATTCCATTAGTAAGATTTACGCCACTGGCATAAAATGTAAACTGTGGTGAAGCAAAGCAACTGTAAAGAGGTGTGAAATGATCAGTAAAGATTCTGTGTTGTCAAGCTTGGGCTTAACTCCCGCATGACAACATGGATTCCATCCTGGCAGCTATGTTGACAAATATAGTGTCTGCATACATATGGTATTATTTTCTTGCTCTGCTCAGAAGTGTCAAATACTTCAATCTATTGCAGAAATCAATTTAACCTGATCGCAGGTATATAATACAAGTTAAAAAATATGAGCATTCTTCTATTATTTTTAGATCTGTTTCATAATCTATCTACCACAAGAACATTAACCGTGGTGCAACAATGTCGTACACTGGAGGGGGTTATGCCCCCTACACTCAGTATGGGCAAACTAACAACCAATTTTCAACAACCTATACACCTGTGAACCAGTCACAGAGTCAATATGGTGTACCAGCATATAATCCATATACTGCACCTTACCAATACCCCTATAATGCACCTTATGGACAAGGGAACAACCCTTATGGAGAATCTAATACCCTAAGTGGAATCTCATACCCACAAATTGGTTCATATGGGCAAGGGCCCATCACTGCACAAGGAGGACAGTACTCAAATGTTGCTCCACCTAATAATTCAAATGGTTCCACTCCAAATAATCAAGCACCCCCGCCCTCGCATAATCAGGCATCCACACCTTCATATAGTCAGGCAGCCCCACCTTCATATACACAGGCACCACCATCTTCATATAATCAGGCCCCGCCACCCAACTATGCAGAGAATACATCTACCTATCAGCAAGCATCTTCCCATCATGAAAGGCCAACCCACCCTCAACGGCCAACCCACCCTCAACGGCCAACCCACCCTCAACGGCCAACCCACTCTCAAGGGCAAACCTACCCTCAAGGGCAAACCTACCCTCAAGGGCAAACCTACTCACAGGGTGCAACCTATCCCCAACAAGGGATTACCTATCCCCAGCAAAACTCCTCCTATGGACAGCAAGGCCCATCATACACACCCAATGAACCCACTTACACGCCACAGGATGAACCATATCCCAAAAATACAAACTCCTATCCAACAACATATGGGCCTCCTATTGGCCCCCAGAAACCCCCAAAACGACCACATATGCCCCCCAGGCTTCAGACAAGTTTCAAACAAGCTAAAAAGACTGCAGCCAAACCGCCACAACCAATAACTTCCATGAAACCACTTCAAGGTGGGAAATCGGCTGTCAGTACGGTCCAGGACCTTGCTTATCAAAATGGATGGACAGTGAATTGGTTTGAAGAATCCGAAACAGGCCCAGCTCATGCAAAGGTTTTCTCAATGAAAGTTACCATGGGACCTTACGAAGTCAGCGGCAGTGGTCGATCGAAAAAACTTGCAAAACAGGACGCAGCCCAATTACTTGCAGCCCAAGTCTCTGGTAATGAAGTAGCTGACATTATGGGACTGCCTGGTTTTACTGGAAGTGCTGGCCAAACCAGTCAGGCTGGAAACACATCGGAAGACTATGGACCTCAGTTACCCCAAGCTGCTGGTCAGAAGACCATTTCAGTGGGGCCATCCGGAGGGGATAACCCTATTTCTACGCTAGATCATGTTGTAAAGAAGCACAAGCTGGGGGAACCACAGTATATTACTGTATGTGAGAATGGACCATCAGCTCTACAGAGGTTTGATATGAAGGTAAAAGTCAACAATATGGAGGCTTCGGGACTTGGTCGTTCAAAGAAAGTTGCGAAGCGTAATGCGGCACAGGCCATGTTGGATCAACTCTCGAGAACACAAACTGGTATTCAACCACCAAAGAAAAGAATTATGTTTGTGAAAGCGTCAAGTGAGACTGCCACGAATACTGGTACTGCTACTGAGAGTTAGACATTAGATTATATACTTTTTCCGAACGATGGCGTAGAGACCATGTGCTGTTAAGTTGTTCAGGCTGTTATTTTCCCGAATGGCTTCTAGGCTATGTTGTACAATATACACATCATCTACCTTGACACCACCCGTTGCCATCTTCTTGAAAAAGGTCAATATCAGAGTGTTCTTTATAATACAGTAATAAGATAATATAAGAATATAAACTATTTACTATTTGCGTTATACTACATTTCTGTGTGATATGTTGAATAATATAATTCCTTATATACCCTTTCTCTGTCTGCGGACTATACAGTACACCTGACAAGTTAATTGTATTGAGGTTTAGATttcgttgttttgtattttagatTTCACTACCGTTACCTTTTACTGacgcatgtgattggttaatctggtagattaaacacatctgattggttaatggtcgcTTAATGGTAGCGCAAGTCAAATCTAAACCTCGCTAGTATGACCTTGATGtacatacgtaaaaacgcacaacttgtggcaaacatgcatgcagcagtcgacttgtggcaatgctgttccaacaacttgtcaacaggatgtgttcgcactgcttgttccccagcttgttgacaagccgttgacaacttgatgcaaggttgttgagctcaacagacttgttacaagttgttccaagaccttgttatcgtcctgtaattcaacaatttgtcaacaagataatGTTGTGACAACtttttgacaagcttgctacaagcctgttgcgaatacatcttgttgccAAGTTGTGAAATTTTTAAGTGTGTAGAGTTTAGAATAAAATCCTTTGGCGTTAGACGAAGTCAGTTATCCTTGGGCATTTTGAGAGAGAAAGAGCTCTGTTATCAtgttttgagtgaaattttagAATTAATCGGAAAATCAGTATTCTTGCTAAATCTCCATGCAGCGGCACAGCCAAATATATAATTCTGGTTATTTGGTATCtaacaaaattaaatatgcGGATGATTTCACGAAATGCTTCTATTTGGAGTGAGTTTTGTCCTGTCGCTGGAAATGGATTTTGTGACTAGTTTTTAGCGGCAACTGGACTTTGTAGCTCAGGGCATGGCCAGGTATTAAAACCTTCAAACGTTCAATCAGACAAATTCTTTCAATacccaaaataaattttaatacccaaaataattttcatgCATTACGTTTCATGTAAAATATCTTTTCTAAACTAGAGTAGCAAACTGCTCCTTGTTTTCTGTTAAAGCTCTCGGTTCATGAAGGAATACTGCGAATTCCACGCCCTTAAAAAGAAAACACAAGATTTTAGCTGACCATGCATTTGTTCAGCTGTGATCTACTGATCTCACTTGACGACAGAGCTACAAAGATCCATGGCCATGAAAGGCTAGCTTATGCCTTAATGTCTTTCATactaaaaatattatatagattatagcgGTTACtaattttcaaagaaaaataaaattatattgggtACCTGTTCCCTTGCTGCTCTTACAAATGATCCATTTGAAGTTATCGTGACTGCTTGTAACTTATCTCCTGTTCCAAATACAATCTGAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8CJ67	Double-stranded RNA-binding protein Staufen homolog 2 OS=Mus musculus OX=10090 GN=Stau2 PE=1 SV=1
Q7ZW47	Double-stranded RNA-binding protein Staufen homolog 2 OS=Danio rerio OX=7955 GN=stau2 PE=2 SV=2
Q9Z108	Double-stranded RNA-binding protein Staufen homolog 1 OS=Mus musculus OX=10090 GN=Stau1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002781 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00035 all species →	dsrm	Double-stranded RNA binding motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR014720 all species →	Domain	Double-stranded RNA-binding domain	Interproscan
IPR051740 all species →	Family	Double-stranded RNA-binding domain-containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46054 all species →	MATERNAL EFFECT PROTEIN STAUFEN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003725 all species →	Molecular Function	double-stranded RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007281 all species →	Biological Process	germ cell development	Interproscan
GO:0008298 all species →	Biological Process	intracellular mRNA localization	Interproscan
GO:0010494 all species →	Cellular Component	cytoplasmic stress granule	Interproscan
GO:0035418 all species →	Biological Process	protein localization to synapse	Interproscan
GO:0043005 all species →	Cellular Component	neuron projection	Interproscan
GO:0043025 all species →	Cellular Component	neuronal cell body	Interproscan
GO:0098964 all species →	Biological Process	anterograde dendritic transport of messenger ribonucleoprotein complex	Interproscan
GO:1990124 all species →	Cellular Component	obsolete messenger ribonucleoprotein complex	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 CAB3981815.1.

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

Expression pattern (RNA-seq)

Transcript abundance of CAB3981815.1 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

6TPM > 0

4Conditions

4.0Max TPM

0.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	0.94	2.98
apical branchlet · Temperature treatment at T0	6	1	0.67	4.03
apical branchlet · Temperature treatment at T25	5	1	0.00	0.00
apical branchlet · Control at T0	4	0	0.00	0.00

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	2.98
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	2.64
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
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
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.03
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977428	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
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
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
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
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.