Gene detail

Detailed information of CAB4013409.1 in Paramuricea clavata

Genomic Location: pcla8_s008111:16465...20719
NR annotation: CAB4013409.1, argonaute-2 isoform X1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PACLA_8A073078

ATGGTGCCTAGTGACATATCCAATATCCCTGCCTCCTCACTCGATGCAGTTAATAAACCGAAAACACCACCTCTAGAATCATATGAAGTAAGTGAGTTAACGAAGACGCTTGAACCGTTGAATATCAGATCGAGACCTCATCTTCGAACTCAACCTTCAAAAGCTGCTACCAAATCGAAAGCTTCCGGACAGCATCCTGGTCCCAGGAGTAAACCCGTAAAAGGCTTTCAGCCTCCTACAACCACTTCTACTCGACCACCCCGGTCAGAAAAAGCAGAACCAAGGCCCCCTCGTCGACCAGACAAAGGTGGTACACTAGGCCGACGAATCAAGCTACGTGTGAACTTTCTTCCTGTGAGTTTGCCAGAAATAGATATTCATCATTACCGTACCGAAATCATCGCGAAAGGCTACGAGTCTGGCAAAGGGTATACAAAGAGGGAAGCTCCCAAGATAATAAAATGCATGGTTGAGCAGTATCAAAACGCTAATCCACATGGTCCAAAACTGGTATATGACAAGAACGGAGAAAATGTATACTGCAAAATACCGATTCCTGGTATTGAGAACAGTCGTGAATACCAGGTTTTGTTTTCCACGGATAATGGTAAGCAACGGGAATACACCGTTAAGATCAAGTGGGTTAGCAAAGTCAGTTTATACGACTTAAACGAGGCACTTAAAGGAAATCGGACAGAGATACCATACGATGCAATGCAAGCTGTAGAGGTCGTGTTGCGACACCTGCCGAACATGAACAGTATTCCGATAGGATCATCCTTTTATAATCATCCAGATGGGCGTGAGAAAGAGCTCGGATTTGGCGTACAAGTTTGGAATGGGACATTCCTTAGTATTCGACCAACGCAATGGAAGATGATGATGTTGAATGTGGATACTTGTTCCACTGTGATCTATAAAGCACAGCCTGTCCTGAATTTTTTGTGTGAGTACTTCGGGTTGGAGAGGCCACCAAGGTATCTTAGTAGCGAACAAATAGAGGATTTCAATGATGAGATTAACGACCTCAAAATTGAGACGATTCATGTCAAGAGGAAACAGAGAGTTGCTGGTTTATCAACCGAATCAGCTAAGAAAAAAATATTCGATTGTGATGGTAAAAGTGTATCTGTGTTTGAGTATTTTAAAGAGAGACATAACATTACGCTTCTGTATCCAGATCTTCCTTGCCTTAAGCTAGGTAACAATGGCGCTTGTATTCCAATGGAACTCTGCAACATTATGGAAGGTCAACGCAAACAAGGGAAACTCACGAAGGAACAGTTACAAACAATGATAAAACACACAGCTCTACCAGCACCTGAACGCCAACAGTTAATCAATAATTTAGTTCGAAGTGCTAAGTTTGATAAAGACGAATTCCTCGCGGACTTTGGTTTTAAAGTTAGTCAAGATTTGCCACGACTAACAGGAAGAGTGTTAAAGCCGCCAACGATTGAATATGGGCAAGCGGAGAAGGAATTGCCAAGAAACGGTGCATGGAACATGCAACACAAATCGTATAAGACGGTTGATTTAAAAGAATGGGCAATAGTTTCGTTCGAGAATCAACGTTTTTTGAATGGTGTAGGTCTAGATAAATTTGTTAGCTCTTTAGTTCAAGCAGGAAGAGATAAAGGCTTTTCCATCCACCCATCCCCTTGCTATCGTGAGTTTATGCATGGATCGGAAAGAATCGGTCGGCTGTTTCAAGATTTATCCCGCCGTTATCCCAATTTGCAACTCATCATCGTTATTTTACCTGGTAAAGGAAACCTTGATGCATATTACGAAGCAGTCAAGTATTTCGGCGACGTCTTTTACGGCATTCGAACCCAGGTAATTAAGGCGAATACAGCCAGCAAGAAAGCTAGTGACAGGCAAACAATGGCAAATATTTGTCTGAAGATTAACGCAAAACTCGGTGGTACGACGTCCATTCTAGACAAACGTGAGAGATCGGAAATACTTGGTCGACCCGTGATTATTTTTGGAGCTGATGTCACACATCCATCACCACGTGACGTGAATAGTCCATCAATTGCTGCTGTCGTTGCTAGTATGGACTCGAACACAAACCTTTACAGTGCTGAAGTGCGCGTCCAAGAACGGCGTAAAGAAGTTATTACGGAGTTGAAGGACATTGTTAAAAATCTCTTGAAAAAGTTTAGGGCAGCAACTCGTGCACAACCTGAAAAAATTATCTTCTATCGAGATGGTGTAGGTGAAGGACAGTTCAAAGATGTCCTCCTTCAGGAGCTTCGCGCAATCCAACTTGCGTGTTACGAATTGCACGAGAGCTTTAAACCAGCCATCACTTTTATTGTTGTCCAGAAGCGTCATCACACCCGGTTCTTTGCTGAAGAAACCAGAGATCAATGCGGAAAGAGTAAGAATATCCCTCCTGGAACGGTCGTCGATACAGATGTATGCCATCCCTATGAGTTCGATTGGTACCTGTGCAGTCATGCTGGTATACAAGGAACTAGTAAGCCAGCACATTATCATGTTTTATACGATGATAGTAATTTTACGTCTGATCAGTTGCAGACCTTGTCTAATCAATTATGTCATACCTACGTGCGGTGCGCCAGAGCTGTTTCCATACCTGCCCCTGCCTACTATGCTCATCACGTAGCATTCCGAGCGCGCTATCATTTAGGAATGCTGACAAGAGGTCGAAGAGGCAATGCTCTTTCGCTTAAGGAGATGTCAGATGCGGTGAATATACACGCAAGAATGACGAATACGATGTATTTTGCATAA

Transcript

rna-PACLA_8A073078

CCATAAGAATATCTTCACTTTGTTAGCCCACAACGCAATCCTCGAGTTTATAAGGTGTTGGGGTTCGATTAAATTTATGTTACCTCTTTTGACACACCCTACCTTTCGTATACGTCACGTCTCTAAATTCTCGAAGTCAAGAGATGGCGGAACGTCAACTGATCTGACCTTAAAGCTATCGCCAGCTATTATTTTCGCTGCGCAAGTTTAAAATATCATAGCGCAATAAATTGTTTGGAATGTGTATGCAGGACCATAATTCTTGATGTGTTTTATTCCAGGAACAAGCACCCCAGAGACATGAAGCATCCACGTCTTTACCACAAACACAATCGAAGGCAGTCGCAACTTTAAAATCAGAACAGAGACGTGTATCTCCATATGATGAAGGTGATGCAAAATCTGCGCAACTCTCAAGTATTAAACCAGAAATTCATGTCTCTCATCAGCAAATGGTGCCTAGTGACATATCCAATATCCCTGCCTCCTCACTCGATGCAGTTAATAAACCGAAAACACCACCTCTAGAATCATATGAAGTAAGTGAGTTAACGAAGACGCTTGAACCGTTGAATATCAGATCGAGACCTCATCTTCGAACTCAACCTTCAAAAGCTGCTACCAAATCGAAAGCTTCCGGACAGCATCCTGGTCCCAGGAGTAAACCCGTAAAAGGCTTTCAGCCTCCTACAACCACTTCTACTCGACCACCCCGGTCAGAAAAAGCAGAACCAAGGCCCCCTCGTCGACCAGACAAAGGTGGTACACTAGGCCGACGAATCAAGCTACGTGTGAACTTTCTTCCTGTGAGTTTGCCAGAAATAGATATTCATCATTACCGTACCGAAATCATCGCGAAAGGCTACGAGTCTGGCAAAGGGTATACAAAGAGGGAAGCTCCCAAGATAATAAAATGCATGGTTGAGCAGTATCAAAACGCTAATCCACATGGTCCAAAACTGGTATATGACAAGAACGGAGAAAATGTATACTGCAAAATACCGATTCCTGGTATTGAGAACAGTCGTGAATACCAGGTTTTGTTTTCCACGGATAATGGTAAGCAACGGGAATACACCGTTAAGATCAAGTGGGTTAGCAAAGTCAGTTTATACGACTTAAACGAGGCACTTAAAGGAAATCGGACAGAGATACCATACGATGCAATGCAAGCTGTAGAGGTCGTGTTGCGACACCTGCCGAACATGAACAGTATTCCGATAGGATCATCCTTTTATAATCATCCAGATGGGCGTGAGAAAGAGCTCGGATTTGGCGTACAAGTTTGGAATGGGACATTCCTTAGTATTCGACCAACGCAATGGAAGATGATGATGTTGAATGTGGATACTTGTTCCACTGTGATCTATAAAGCACAGCCTGTCCTGAATTTTTTGTGTGAGTACTTCGGGTTGGAGAGGCCACCAAGGTATCTTAGTAGCGAACAAATAGAGGATTTCAATGATGAGATTAACGACCTCAAAATTGAGACGATTCATGTCAAGAGGAAACAGAGAGTTGCTGGTTTATCAACCGAATCAGctaagaaaaaaatattcgaTTGTGATGGTAAAAGTGTATCTGtgtttgagtattttaaagagaGACATAACATTACGCTTCTGTATCCAGATCTTCCTTGCCTTAAGCTAGGTAACAATGGCGCTTGTATTCCAATGGAACTCTGCAACATTATGGAAGGTCAACGCAAACAAGGGAAACTCACGAAGGAACAGTTACAAACAATGATAAAACACACAGCTCTACCAGCACCTGAACGCCAACAGTTAATCAATAATTTAGTTCGAAGTGCTAAGTTTGATAAAGACGAATTCCTCGCGGactttggttttaaagttagtCAAGATTTGCCACGACTAACAGGAAGAGTGTTAAAGCCGCCAACGATTGAATATGGGCAAGCGGAGAAGGAATTGCCAAGAAACGGTGCATGGAACATGCAACACAAATCGTATAAGACGGTTGATTTAAAAGAATGGGCAATAGTTTCGTTCGAGAATCAACGTTTTTTGAATGGTGTAGGTCTAGATAAATTTGTTAGCTCTTTAGTTCAAGCAGGAAGAGATAAAGGCTTTTCCATCCACCCATCCCCTTGCTATCGTGAGTTTATGCATGGATCGGAAAGAATCGGTCGGCTGTTTCAAGATTTATCCCGCCGTTATCCCAATTTGCAACTCATCATCGTTATTTTACCTGGTAAAGGAAACCTTGATGCATATTACGAAGCAGTCAAGTATTTCGGCGACGTCTTTTACGGCATTCGAACCCAGGTAATTAAGGCGAATACAGCCAGCAAGAAAGCTAGTGACAGGCAAACAATGGCAAATATTTGTCTGAAGATTAACGCAAAACTCGGTGGTACGACGTCCATTCTAGACAAACGTGAGAGATCGGAAATACTTGGTCGACCCGTGATTATTTTTGGAGCTGATGTCACACATCCATCACCACGTGACGTGAATAGTCCATCAATTGCTGCTGTCGTTGCTAGTATGGACTCGAACACAAACCTTTACAGTGCTGAAGTGCGCGTCCAAGAACGGCGTAAAGAAGTTATTACGGAGTTGAAGGACATTGTTAAAAATCTCTTGAAAAAGTTTAGGGCAGCAACTCGTGCACAACCTGAAAAAATTATCTTCTATCGAGATGGTGTAGGTGAAGGACAGTTCAAAGATGTCCTCCTTCAGGAGCTTCGCGCAATCCAACTTGCGTGTTACGAATTGCACGAGAGCTTTAAACCAGCCATCACTTTTATTGTTGTCCAGAAGCGTCATCACACCCGGTTCTTTGCTGAAGAAACCAGAGATCAATGCGGAAAGAGTAAGAATATCCCTCCTGGAACGGTCGTCGATACAGATGTATGCCATCCCTATGAGTTCGATTGGTACCTGTGCAGTCATGCTGGTATACAAGGAACTAGTAAGCCAGCACATTATCATGTTTTATACGATGATAGTAATTTTACGTCTGATCAGTTGCAGACCTTGTCTAATCAATTATGTCATACCTACGTGCGGTGCGCCAGAGCTGTTTCCATACCTGCCCCTGCCTACTATGCTCATCACGTAGCATTCCGAGCGCGCTATCATTTAGGAATGCTGACAAGAGGTCGAAGAGGCAATGCTCTTTCGCTTAAGGAGATGTCAGATGCGGTGAATATACACGCAAGAATGACGAATACGATGTATTTTGCATAAAGATGCACAGTCAAGCCAATGGAGTTTCTGTTTAAAAATTACTTGTATTTTGAACAGTTACGTTGTCTTTTTACGGCAGGGCTAAAACCTTGATTTTCGGAAACAAAACTATAAacgtttattatatggcatttattggcatttatacttgaaaaaaAACCCAAGAAACTAAGAAAGTTAtaatttgaaatgcatattaatagcgtggtacacatttggtcgaagaaaacaaaaaataccaatgtaatTCAATTAAATACCaatttccactaaaaaccattcgcaaatatcttattaataacaaattaaattataatttcaaattttcaattagttttgatGTTTTagaatgcatgcgtttgtttttacaaccgctgaaagtgcttctcagccaatcaccggaaatgcttgccatataataaaagcctatattcacttcgccttcggctcagcgaatataggcttgtaatcacctcgccttcggcggctaattgttaaatataccaAATGCTAGATGCGTTTACTCACCCAGTGCACTTTTCCAACTTTTCCATTTATTAGCTTGTTGATCCTATTTGTAGCTCCAAATCACTCATGACTAGaaatacagtgtgtataaaaaaaactgaccCTTTCacattcaaattagctataacatATTgcagtaatttgacagctctaattgctttgaacaCAAGGTGTTGTACTCGATCacgggacaaaactcaaagaaataaaaattagaaaatttaaattttaccaTACGTCAccatacaacgttatacaagactatacaacaatatataaggctatacgacactgtacggcactatacaacgttatacaagactatatgacactatgcaagactatacaacactatactaCACTATAGACGACTATTATACAAGaataattactgacggtcataataacctattgttttctctctgcattatatcagcgaatgtcgagaagttttagcgttcttctaaaaaacgggagcggtcttttttaattgtagggaaattcccagg

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O77503	Protein argonaute-2 (Fragment) OS=Oryctolagus cuniculus OX=9986 GN=AGO2 PE=1 SV=2
Q8CJG0	Protein argonaute-2 OS=Mus musculus OX=10090 GN=Ago2 PE=1 SV=3
Q9QZ81	Protein argonaute-2 OS=Rattus norvegicus OX=10116 GN=Ago2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000826 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02170 all species →	PAZ	PAZ domain	Domain	Interproscan
PF16488 all species →	ArgoL2	Argonaute linker 2 domain	Family	Interproscan
PF02171 all species →	Piwi	Piwi domain	Family	Interproscan
PF08699 all species →	ArgoL1	Argonaute linker 1 domain	Domain	Interproscan
PF16486 all species →	ArgoN	N-terminal domain of argonaute	Domain	Interproscan
PF16487 all species →	ArgoMid	Mid domain of argonaute	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR003100 all species →	Domain	PAZ domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR045246 all species →	Domain	Argonaute-like, PIWI domain	Interproscan
IPR032472 all species →	Domain	Argonaute linker 2 domain	Interproscan
IPR003165 all species →	Domain	Piwi domain	Interproscan
IPR014811 all species →	Domain	Argonaute, linker 1 domain	Interproscan
IPR036085 all species →	Homologous_superfamily	PAZ domain superfamily	Interproscan
IPR032474 all species →	Domain	Protein argonaute, N-terminal	Interproscan
IPR032473 all species →	Domain	Protein argonaute, Mid domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22891 all species →	EUKARYOTIC TRANSLATION INITIATION FACTOR 2C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003727 all species →	Molecular Function	single-stranded RNA binding	Interproscan
GO:0004521 all species →	Molecular Function	RNA endonuclease activity	Interproscan
GO:0016246 all species →	Biological Process	regulatory ncRNA-mediated post-transcriptional gene silencing	Interproscan
GO:0035198 all species →	Molecular Function	miRNA 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
K11593	ELF2C, AGO; eukaryotic translation initiation factor 2C	-	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4013409.1 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

12TPM > 0

4Conditions

18.9Max TPM

2.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	1.42	4.25
apical branchlet · Temperature treatment at T0	6	5	7.09	18.86
apical branchlet · Temperature treatment at T25	5	2	0.79	1.98
apical branchlet · Control at T0	4	1	0.20	0.81

Per sample · hover a bar for the full sample record

Show the sample table (21 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	4.25
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.34
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.54
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.36
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	18.86
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.80
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.56
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.63
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.71
SRR19977436	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	1.98
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.98
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
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.81
SRR19977442	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.

Co-expression network

Genes whose expression across the transcriptome samples of Paramuricea clavata tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	8	CAB3999630.1	0.924918041530981
Negatively correlated	8	CAB4003069.1	-0.56218902572968

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Paramuricea clavata, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →