Gene detail

Detailed information of BRAKERKREP00000023760.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: WP_013392618.1, ribonuclease R [Achromobacter xylosoxidans]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000023760

ATGCAAAGCAGTTCGCCATCATCTCTGCGTATCGTCTTGGGCCCGTGGGAGCGCCTCGGGGCAGAAGCCAGCCGCATacgttttgaagtttttgtacGTGAACAAGGCGTCCTTCCTGAGATAGAGCTGGACGACCGGGACGCCGTTTCTTTGCATGCTATTGCCTATACCCACAATCGGGCACCGGTCGCTACTGGCCGCCTGCTGCCCGACGGTCATATTGGCCGCATCGCAGTGCTGAGGCCGGCGCGGGGGACTGGCGTAGGTGGCCAGGTGCTGGACGCGTTGATTGAAGAAGGCTATCGCCAAGGTCATTCCAGGTTGGTGCTGCATGCGCAGATGCATGCCCAAGGATTTTACGAGGCTCGAGGCTTTGTCGCTCAAGGCGAGGCGTTTATGGAGGCTGGGATCGCGCACGTCGTAGGGGTGCGACAATGCGGTTTCAATGCGCGATTTCAGCGCGGCTTCATTGCGTTGGTGCCCAGGAGAGGACTCGAACCTCCACGGAGTTACCCGCTAGTACCTGAAACTAGTGCGTCTACCAATTCCGCCACCTGGGCTATTTCAAGACAAACTGCCATTGTAACTGCCGAAGTCGGCATGTCAATTGCCTATATAGCCAGGCTCAACGTCGCGGGGCAAGAGAAGCTGCGCAATGTAAATGGAATTTCAGCTTTGGCGAAACGATCGAACGAGGAAAATAACAATAGATCTTTTTCCGTGTTGCCCGATGCGCCTGCCGACTTCGATCCCGATGTTCCTAGTCGTGAAGCCATATTGAGAGCATTGCGTTCGGTCGGCACGCCCTTATTGCCGGCAGAACTGGCGCAGCGCATGGGGGTGGAGCGTCCCGCCACGCTCGCCGGCTTTGAGCGACGACTCAGTGCTATGGAGCGTGATGGACAACTTTTGCCCAATCGTAAAGGCGTGCTGTTGCTGGCTACAAAACTGGATTTCGTCGCCGGTAAAGTGCAAGGCCATCGCGACGGTTTTGGCTTTTTATTGCGTGATGACGGCGGCCCAGACCTGTTTCTTTCACCACGCGAAATGCTCAAGGTTCTGCACGGTGATCGTGTGCTGGCCAAGCCTGCGGGCGAATACAGGGGCAAGCCCGAAGGTACAATTGTCGAGGTCCTCGAACGACGTACCAACAAGTTGGTAGGACGGTTTTTGCACGAACACGGCTTGTCCATTGTGGTGCCGGAAGACCAGCGCATTAAGCACGACATACTCATTCCTCCAAGTGACACTCACGGTGCCCAACACGGACAAGTGGTAGCCGTAGAAATCATCGAACAGCCCACCCGGCATACGCAACCACTGGGCCGTATATCAGAAGTGTTAGGCGAAATCGATGATCCCGGTATGGAAATTGAAATTGCCGTGCGCAAGTTCGATGTGCCGGTGGCGTTTTCCGAGGCGGCCCGCAAGCAAGCAGCGCTTTTACCCGACGCGGTACGCAAAACAGATCTTAAGGACCGCGTGGATTTGCGCGATGTGGCCTTCATCACCATCGATGGTGAAGACGCACGCGACTTTGACGACGCTGTCTATTGTCAGCCCATAGAACTGGGCACGGGTAAGCGCAAACGGCCGGCCTGGCGTTTGCTTGTCGCCATTGCTGATGTAAGCCACTATGTGCGGCCCGGTGATGCGCTGGACGATGATGCGCGTGAGCGTGGCACGAGCGTGTATTTTCCACGACGAGTCATTCCTATGTTGCCGGAATCGCTCTCCAATGGCTTATGTTCTCTTAATCCGCAGGTTGACAGGCTGGTATTGGTTTGTGACATGGTAATTCCGGCGTCGGGTGCTAAGGCCGGCACCGTGACAGCCTATCAGTTCTACGATGCGGTGATACATTCCCAGGCCCGTACCACTTACACCCATATATGGGCGGCGCTGCAGCAGCCTGGAGGGCCAGCGGCGAACGCGATCGAACTGCTTATGCCCCACGTGCGGGATCTGTACGAGCTTTATCAGCTATTGGCGCAAGCGCGCAAGAAGCGGGGCGCCATTGATTTTGATACGGTCGAGACAAAAATCCTATGCAACGACCTGGGCCGCATCGAGCAGATAGTGCCGGCGATGCGTAACGATGCGCATAAGCTCATCGAAGAATGCATGTTGGCTGCTAATACCTGCTCGGCCGACTTTATGGCGCGTAGCAAGCATCCCGGACTCTATCGCATACACGAAGGACCTACGCCAGAACGATTGCAGTCGCTACGAGAGTTTCTGCGTACCTTGGGCTTGTCTTTAGGCGGCGGCAGCGAACCCACGGCCAAAGACTATGGTGAGTTTCTCGATACGGTGCGCAACCGCCCCGACTATCCCTTGCTGCAAAGCATGTGTCTGCGGTCTATGCAGCAAGCTATTTACAGCCCGGAGAATGTGGGCCACTTTGGCTTAGCTTATCCCGCCTACAGTCATTTCACCTCGCCGATCCGCCGCTATCCGGATTTGCTGACGCACCGCGTTATCAAGGCCTTGTTGCATAGGCAGCGTTATGTGCCCGAACTGGAAGACCAACCCATTGTGATAGGGCACAGTCAACGTGAGCACGAACAGGCTCTGTGGGAAAAGCTGGGCCTCCTTCTTTCGGCCAGCGAACGCCGTGCCGATGGCGCATCGCGCGATGTCGAGGCTTGGTTGAAGTGTTGGTTCATCAAGGAGCGCGTGGGCGAGGATTTCAGCGGTATCGTGACGGGGGTGGCCAGCTTTGGAATTTTTGTCACTTTAGATACGTTGCACGTAGAAGGGCTAGTGCATGTCTCTGAACTCGGCGGCGAGTATTTCCAATTCAACGATGCTTTGCACGAACTGCGCGGTGAGCGCACCGGCCTGCGCTATCGTTTAACCGACAAAGTCCAGGTCCAGGTCTCGCGTGTCGACCTGGAGGCGCGACGCATCGAATTTCGCCTCGTCAAGGGGACTAGCTTTGATGCTTTGCGTAAGGCGGCTGCGCGCGGGCCGATCGAACCGGTGcgcaagttaaaaaaagccGCCGCGCCCAAACCTGCCGCCTTAAAAGGACAAACTGCGAAACAGCGGCGTGCCGAAGACAAAAAGGCGAGCACGCCGCCGAAGCCACCTAAGTCATCCCGGCGAGCCAGTACgacagtaaataaaaaagcccTGCGTACGCGTCATTGA

Transcript

BRAKERKRET00000023760

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P44907	Ribonuclease R OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=rnr PE=3 SV=1
P21499	Ribonuclease R OS=Escherichia coli (strain K12) OX=83333 GN=rnr PE=1 SV=2
P30851	Ribonuclease R OS=Shigella flexneri OX=623 GN=rnr PE=3 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001458 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08206 all species →	OB_RNB	Ribonuclease B OB domain	Domain	Interproscan
PF17876 all species →	CSD2	Cold shock domain	Domain	Interproscan
PF00773 all species →	RNB	RNB domain	Domain	Interproscan
PF13673 all species →	Acetyltransf_10	Acetyltransferase (GNAT) domain	Domain	Interproscan
PF00575 all species →	S1	S1 RNA binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR001900 all species →	Domain	Ribonuclease II/R	Interproscan
IPR013223 all species →	Domain	Ribonuclease B, N-terminal OB domain	Interproscan
IPR011805 all species →	Family	Ribonuclease R	Interproscan
IPR050180 all species →	Family	RNR Ribonuclease	Interproscan
IPR003029 all species →	Domain	S1 domain	Interproscan
IPR011129 all species →	Domain	Cold shock domain	Interproscan
IPR022966 all species →	Conserved_site	Ribonuclease II/R, conserved site	Interproscan
IPR040476 all species →	Domain	RNase II/RNase R, cold shock domain	Interproscan
IPR000182 all species →	Domain	GNAT domain	Interproscan
IPR016181 all species →	Homologous_superfamily	Acyl-CoA N-acyltransferase	Interproscan
IPR004476 all species →	Family	Ribonuclease II/ribonuclease R	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23355 all species →	RIBONUCLEASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004540 all species →	Molecular Function	RNA nuclease activity	Interproscan
GO:0004518 all species →	Molecular Function	nuclease activity	Interproscan
GO:0000175 all species →	Molecular Function	3'-5'-RNA exonuclease activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0016747 all species →	Molecular Function	acyltransferase activity, transferring groups other than amino-acyl groups	Interproscan
GO:0016070 all species →	Biological Process	RNA metabolic process	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
K12573	rnr, vacB; ribonuclease R	EC:3.1.13.1	Transfer RNA biogenesis	ko03016	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023760.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00	0.00
unannotated	1	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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.