Gene detail

Detailed information of CAB4034971.1 in Paramuricea clavata

Genomic Location: pcla8_s022856:3536...5680
NR annotation: CAB4034971.1, poly(A)-specific ribonuclease PARN-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A044474

CGTTTCTTTCactttttatatcaaaacaaaAGTGCGACAAAAATCATCAAAGTTAGAACAAAAAGTGAAATATTTCAAGCTGAAATTGATAACTAGTTCAGCCTAGAATGGAAGTGACGAGATTGAATTTCAAGGAagttttacccgtaatttctaacGCCATAGAAGACTCGTCGTTCATTGCAATTGATGCTGAATTCTCTGGATTGACCGCTAGGAAACGCGAGAATGCTATGGACACGTGTGACGAACGATATCAAAAACTTATCAATGGCATTAAAGACTTCACTATTGTGCAGTTTGGTATATGTACTTTTAGCTGGGACGACGAACAGCAACAGTATATAGCTAAACcttttaacttttatatattTCCAAAACCTTACAACAGGCAAATGCCAGATATGAGATTTTTATGTCAAAGTTCGAGCCTTGATTTCTTGGCTGGGCAAGGGTTTGATTTCAACAAGTGGATCACCCAGGGTGTACCGTTTCTTTTGCCACCAGACGAGGGTCGGCTTCGACGGATGGTGGGCGCATACCACGATCAAGCCACGCCCAACGGTGCTCCTTCCACGCCGGAAACAGAGAAGGCGATACCCATTCCACCTGCATTTGAAAAAACAGTCGAACTGATTATGAAGAAAGTTGAGAAATTTATTGAAGATCCTGAGCAGAAATTGTTAAGTTTGCCGCCATCGAGCCCCTTGGTGCGTAAGCTGGTTTATAGCTCTGTTAAAGCTGCTCATAAAACCGGACTTCATTTAGAATCCAAAACGAACGAAGATAAGGATAAATTCATAATGATCACCAAATGCTCGGAACAAGAAAAGAAGGATTTGGAAAACCAGAAGTTTGATAAGGAACAAGTCGAGGTTGAACAAGCAGTTGGGTTTGCGAAAGTGATACGCCTTCTTTCGAAGTCAGGGAAAGTTATTCTGGGTCATAATATGTTGTTGGATCTTTTGCATATGATACGATTATTTGTCGCCCCACTGCCGAACAATCTTGATGAGTTCAAAGCTCTCGTTAAGGGCATTCTACCAAGACTAATCGATACTAAAGTCATGGCAAGTACCGAACCTTTGCAAGGCTACTTTCCACTTTCCCATCTCCAGGAAGTCTACAAGAAAAGTTCAGAAGCTCCATTTGTGAAGCCAAATGTGTTGTTCACAGAGGAATTTGAAGACTACTCCAACAGCTCGAAGGCTCATGAAGCTGGCTTTGACGCTTACATGACCGGGGTAGCATTTATTGCAATGGCCTCCTTCCTGGAGAAACAACGTGATGGCAGCATGCCTTGTGCAGAAATGGATTTTGACATTATCAAACCGTTTTTGAACAAAATCTTTCTTTTTCCACGAATGGAAGACATTCCGTATCTTATCCTGGACGGTAAGGACTTGACTCCGAGCCGGGATCATGTTTTTCACATTGAACACCCGGACAATTGGCAGTTCTCGGATATCCAGAAACTGTTCAAGGATTTTGGGTATGTTTACATTACAAAGGTTAACGGGAGTTCAGCATTTGTTTCCGTTGCGAAGCGTGAACGAGCAACCAAGGTTATGCAGAAGTTGGATAAAGATAATTTACCATACAGAATTCAGACGTACAAGAAGTACCATGGtattgatggtgatgatgatggtgatgatgatctTGCCCTTGATGGTGGTGGCGATGTTAAAGATGATATAGATGGTAAAGATGGTATAGATGGCCATGGTTCATCACTCAATCAAAGTTCTACCTCCACACCAAGTTTCGACACTCCCAGTAAAACACCAGAAACCGTCTCATCCAAGCGATCGAAAGATGATGTTTCTTCATCCGAGGTTGAGGAAGGCGAGCTTCCTGACTCACCCGAACCAGCAAAGAAGAAACTAAAAGGTCAGCATACCTATTTTGAAGAGCCTAATGAGTGGTAGTATTGTTAAGAGTTAAGACgtaaacatatgcaaattacATTGTAGCTCTGTGCTAATTATGGCAAGAAGTaagaatttgactataaaataatGTGATAAAATACACTTGCTTATATACATgttataaaactcttaatcactttttaatcactattttgtagttaaatagtgattaactctcaaataggcgcttcttattggatgacgtttgcac

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8VDG3	Poly(A)-specific ribonuclease PARN OS=Mus musculus OX=10090 GN=Parn PE=1 SV=1
Q90ZA1	Poly(A)-specific ribonuclease PARN OS=Xenopus laevis OX=8355 GN=parn PE=1 SV=1
O95453	Poly(A)-specific ribonuclease PARN OS=Homo sapiens OX=9606 GN=PARN PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001811 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08675 all species →	RNA_bind	RNA binding domain	Domain	Interproscan
PF04857 all species →	CAF1	CAF1 family ribonuclease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR051181 all species →	Family	CAF1 family poly(A)-specific ribonucleases	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR036867 all species →	Homologous_superfamily	R3H domain superfamily	Interproscan
IPR001374 all species →	Domain	R3H domain	Interproscan
IPR014789 all species →	Domain	Poly(A)-specific ribonuclease, RNA-binding	Interproscan
IPR006941 all species →	Family	Ribonuclease CAF1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15092 all species →	POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000175 all species →	Molecular Function	3'-5'-RNA exonuclease activity	Interproscan
GO:0000289 all species →	Biological Process	nuclear-transcribed mRNA poly(A) tail shortening	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004535 all species →	Molecular Function	poly(A)-specific ribonuclease activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006402 all species →	Biological Process	mRNA catabolic process	Interproscan
GO:0046872 all species →	Molecular Function	metal 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
K01148	PARN, PNLDC1; poly(A)-specific ribonuclease	EC:3.1.13.4	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4034971.1 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

9TPM > 0

4Conditions

9.9Max TPM

1.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	4	3.18	9.25
apical branchlet · Temperature treatment at T0	6	3	2.72	9.93
apical branchlet · Temperature treatment at T25	5	1	0.27	1.36
apical branchlet · Control at T0	4	1	0.95	3.82

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	9.25
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	5.54
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	3.87
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.41
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
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	9.93
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	4.52
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	1.88
SRR19977426	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	1.36
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
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	3.82
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.