Gene detail

Detailed information of BRAKERKREP00000002011.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_002160561.1, poly(A)-specific ribonuclease PARN [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q90ZA1	Poly(A)-specific ribonuclease PARN OS=Xenopus laevis OX=8355 GN=parn PE=1 SV=1
P69341	Poly(A)-specific ribonuclease PARN OS=Bos taurus OX=9913 GN=PARN PE=1 SV=2
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
PF04857 all species →	CAF1	CAF1 family ribonuclease	Family	Interproscan
PF08675 all species →	RNA_bind	RNA binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR006941 all species →	Family	Ribonuclease CAF1	Interproscan
IPR036867 all species →	Homologous_superfamily	R3H domain superfamily	Interproscan
IPR014789 all species →	Domain	Poly(A)-specific ribonuclease, RNA-binding	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR051181 all species →	Family	CAF1 family poly(A)-specific ribonucleases	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:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004535 all species →	Molecular Function	poly(A)-specific ribonuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006402 all species →	Biological Process	mRNA catabolic process	Interproscan
GO:0046872 all species →	Molecular Function	metal ion 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

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 BRAKERKREP00000002011.1 across 29 RNA-seq samples of Hydra viridissima. 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.

29Samples

13TPM > 0

7Conditions

45.9Max TPM

5.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	4	4.80	45.91
Whole	6	5	3.79	5.27
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	3.95	3.95
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	4.18	4.18
symbioic hydra M9 strain · symbioic hydra rep1	1	1	3.83	3.83
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00	0.00
unannotated	1	1	40.51	40.51

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	45.91
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	34.58
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	3.87
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	2.08
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	5.27
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	4.73
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	4.70
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	4.29
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	3.75
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	3.95
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	4.18
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	3.83
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	0.00
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	40.51

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 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.