Gene detail

Detailed information of BRAKERKREP00000014816.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047143384.1, RNA exonuclease 1-like [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000014816

ATGAGTGATGAAGCAATTCGTAACTATATttcatcaaatgaaaatgatgataCCACGTATAAAGCTGAGAAAGAAAGGTATCATTTATATGCTTGTGGTGGTTGCCCATTTGCAAACatGGCAACTATTGTGCTTGCGCTGAAAGGTCTTGAAGATGTAATATCAGTTAGCTTAGTTGATCCTGTATTTGATGCTGAAACTGGATGGAGATTTACACCTGATATAAGTGGTTGTACTGATAATGTATGTGGGAAAATCTACTTGAAGGATGTTTATGAAATGTCACATCCAGAGTATCAAGGAGTAACCTCTTTAGGTTACAGTAAACAGACAAAAATTCCTGttctttttgataaacaaacaaagaaaattgttaacaATGACTTTATAGATATTATGAAAATGCTAAACACACAGTTTAACAAGTTCTCACCATCAGAGAAACACGCACTTATCAACATTTATCCAGaagataaacaaaatgatattgataaaatgaatCAGTGGATCAATGAtgATATCATTATGGGTGTTTACAAATGTGGATCTGCAAAACTTCAGGAAGATTATGATAGACATGTTAATAAGCTGTTCGACAGTCTAGATAGGgtGGAAGATATTCTTTCAAAGAGCAGGTACTTAACTGGAAATACTATTACCTTGGTAGATATTTGCTTGTTTTCATGTCTTGTTCGATTCGATAGCTGTTATTATACATTATTCAAGtGCTCTAAACAAATGATAAGCTGGTACAAAAACATATGGGGATATACACGAGATATTTACCAAACTGGAACAATCAAGAACATGATCCACTTTGACCATATCAAGTCTTTGTATTGGgACCATCCTCCCTCTATAAAATTTGACGTTGATGAGCTTTTTTCTTTGGGGGGTAAGCGACCAATGGGTTCATCATTAAATATCAATGACATTCGCGCCCTTCTGTTAATTACTGTGACAGACCCAAATTATGTAGTGGTTCCAAATTGGTGTCAGATTAAAAGTAGAAACAGAATTAAGCGATCAATCTTTTTAATGGTGGGTGGTGTTTCAGAGGATGATTTTACACTGAATGTAgattgttttccatttttgacaaaatgttTTGGCAAGCATATTCCTGTTCGAAATGAAGGCTCTGATTACATGCTCAAGTCTCCTTTAGAAAGCTACCTAATGTACAgcttgtcaaaaaaaatgctgcaaaGACAGTTGATGGAGAAAGAAAATGACAAAgATTCTGAACTTGACTTTCATGAGTACATTTTAAGTGACTATCAATTGAAAGTGAATGATTTCCCTGACTGGAACTCAGCTGCTCTTGAACATGGTGTTGTTTCCACTCGAAAAAACAATGAGGTGGTTCGtgctcataaaaaaagtaaattgctAGCAATCGACTGTGAAATGtgCAGTACTGCTGGTGATAAGCGTGCACTAACTCGTGTGTCTATTGTGgatgaaaacttaaaagtagTTTATGATCAGCTTGTTCAACCTGATAGTCCTATTACTGACTATCTTACACAatttagtGGGATAACTCCAGAAATTCTACATGGGGTAACTACTACATTGCAAGATGTGCAAACAGATTTGCTAGGAATCATCCAGCCTGATACAATACTAATTGGCCATTCTCTTGATTTTGATTTGCGCTCATTAATGcTTCACCATGACAACATTATTGACACATCTGTATTGTATGTAGATCAACGTGGACCAAGATATAAATCATCTCTACGTTTTCTTGTTAAAACTTACCTGAAtcgTGATATTCAAAACACAGAAAAAGGGCATTGTTCCATAGAGGATGCTAGAGCTTGTATGGAGCTTGTCAaactaaaagttgaaaaagGACCATCATTTGGGAATCCTCAAGTTGAAAGAGAAAGCATATTCGACGGTTTAACACGCGCTGGAAAGAAAGgcGTGATCATGGATGCGGCAAATATCGTTCGTCAGTATGCGCATGGAAACAATCACGGAATCGCATGCGCTTCAGATGAgcagGTCGCATCAAATGggaaaaagtttgtaaatacCCTCGACTTTACTTTCTGTCATTTTAGAAGCTATGAGCAACTGTTAAagtCTGAAGTTGTTATCACCGAAAAAGAACGCAAGGATACTCTACGAAAGTTAGATGAATATATTTCCGAGGTGATAACAGTGGTGGAGCCATGCTGCTTAGTTGTAGTTGCATTGAGTAGTGGATTCATTCCTTCAAAGACGatgaggTTGCTTAGAGACAAAGAGGAgcgaaaaaaagaagaagtaaAGAAAGCATTGAAATTAGCTAAACAAGGCGCATGCTTCGTAAAAATCACCTGA

Transcript

BRAKERKRET00000014816

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P53331	RNA exonuclease 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=RNH70 PE=1 SV=1
Q8L7M4	Small RNA degrading nuclease 5 OS=Arabidopsis thaliana OX=3702 GN=SDN5 PE=2 SV=2
O94443	Uncharacterized exonuclease C637.09 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC637.09 PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002364 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13409 all species →	GST_N_2	Glutathione S-transferase, N-terminal domain	Domain	Interproscan
PF13410 all species →	GST_C_2	Glutathione S-transferase, C-terminal domain	Domain	Interproscan
PF00929 all species →	RNase_T	Exonuclease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013520 all species →	Domain	Exonuclease, RNase T/DNA polymerase III	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR004045 all species →	Domain	Glutathione S-transferase, N-terminal	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR034922 all species →	Domain	RNA exonuclease 1-like, exonuclease domain	Interproscan
IPR047047 all species →	Domain	Glutathione S-transferases Omega-like, C-terminal	Interproscan
IPR016639 all species →	Family	Glutathione S-transferase Omega/GSH	Interproscan
IPR010987 all species →	Domain	Glutathione S-transferase, C-terminal-like	Interproscan
IPR036282 all species →	Homologous_superfamily	Glutathione S-transferase, C-terminal domain superfamily	Interproscan
IPR036249 all species →	Homologous_superfamily	Thioredoxin-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32419 all species →	GLUTATHIONYL-HYDROQUINONE REDUCTASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004364 all species →	Molecular Function	glutathione transferase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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
K14570	REX1, REXO1, REXO5, RNH70; RNA exonuclease	EC:3.1.-.-	Ribosome biogenesis	ko03009	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000014816.1 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

2TPM > 0

7Conditions

0.3Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	0	0.00	0.00
Whole	6	2	0.08	0.31
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	TPM
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	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
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134060	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
SRR21134064	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
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	0.31
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	0.19
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058807	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	0.00
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.00
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.00
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	0.00

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.