Gene detail

Detailed information of BRAKERKREP00000001427.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_012556041.2, exosome complex exonuclease RRP44 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001427

atgcaaagaTCAAAGACATTTGTCAAGAAAACTCGTAAAGGTGCTATTGTCAAAATAGTCCGCGAACATTACTTGCGAGATGATATATGGTGTGGGAGTGAGGGATGTAATCAATGTGAAAATGAAACTCCTACTCTTAGCTCTAAGCCTGACATGCCTTCAACTTTATGTAATTTTCCACATTATTTGATACTTGACACCAATGTTGTTCTTCATCAGaTGGACGTTATTCAagatgaagtttttaaagatataatatTACTGCAAACCGTTTTACAAGAGGTTAAGCATCAAAGCTATACTGTATATAAAAGAATTCGTGAAGTTATAGCAATGAAACAAAAACGAGTATATGTCTTTTCAAATGAGCATCAtatAGACACTTTTACAGCTCGTCGGAAAGGAGAAACATCCAATGATTACAATGATAGATGCATTAGAGTAGCAGCTAGtttttttgagaagCACATGCGAAACTTTGgtgcaaatgttttaaataaaatcacagTTGTGCTTTTAACTAATGACAAgctcaataaacaaaaagcgCAGAGTGAAgggataaaatcttttacagtTGATGAATAtgtgaaaagtttaaatggaTATTCCTATTTGATTGACAAATTAGCTAAAGCTGTATACTTAGAAAAGactgAAGGAAATGCTATCTTTCCAGAACATTTACCACTTTCAGATATTCAAAGTGGCATAAAGGCTGGAAAATTTCTACAGggaacattttttgcaagtaGgGAAAATTATATGGAAGCTACCGTTCGTGTTCCAGGTAGAGAAAATGAGattttcctGCAagggttaaaaaatttaaatcgtGCAATTCAAGATGACATTGTGGCTGTGGAAATTTTGCCTGAAACTGAATGGGTAGCTCCATCCTCACTTAttcttgaagaaaaagatgaaGAGCTAGATGAAGAAGAACAAGATAAGAGGattgaagatgaattcaaaaaacaagcaaaaaaacacCTCAGAGAAACAGGAAAGatTGTGGGGATTATAAAGAGAAATTGGAGGCCTTACTGTGGTATACTGTCTCCAAATGGAAACGCAAAAggttTGAGGCATATGTTTGTAGCTGCAAACCGACAGATTCCCCGCATTATGATTGAATCAAGGCAGGGAGAACTTCTTCAGCAAAAGAAGATTATTGTAAGCATAGATGGATGGCCTAGAAACTCCAGATATCCTTTGGGTCATTATGTAAGAGATTTAGGAGAAAGTGGAGATAAAGCAACAGAGAAAGAGGTGTTACTCCTGGAGCATGATGTACCTCACCAGCCTTTTTCTCAGCAAGTTTTAGATGATCTCCCAAAACTCCCTTGGCGTATTACAGAGCAGGATTATTTAGTGCGTCATGATTTACGTGAACTTAACATATGTAGTATTGATCCTCCTGGATGCACAGATATAGATGATGCATTGCACTGGCGACCTTTAGAAAATGGAAACTTTGAATGTGGAGTACACATAGCTGATGTTTCACATTTTGTAAAGCCTGGAACTCACATTGATGAAGAAGCTAAACAGCGTGGTACTACTGTGTATCTTGTTGATcaacGAATTGACATGATACCAGAGTTGCTAAGTTCAGATCTATGCTCACTTCACGAAAAGGAAGAAagatttgcttTTTCTTGCATATGGGAAATGACTCGAGAGGCAGAGGTTGTTACTGttaactttgtaaaaagtgtaatttgctcaaagGCTGCATTAACATATGCAGAAGCACAAATGATTATCGATGACAATACTAGAGTAGACCCGATTGCCATTTCAGTTCGGAATCTAAATGAGTTagctaaaaaactaaaagctaAAAGAAAGGAATTTGGagcGTTAACATTAGCATCACCAGAAGTTCGTTTTCATATTGATAGTGAAACCCATGATCCTATTGATATGCAGAAAAAAGAACTAAGAGATACTAATTCTCTGGTAGAGGAATTCATGTTGCTAGCAAACATTTCTGTGGCAAAGAAACTATATGAACACTTTCCGCAGCATTCAGTTCTCAGAAAACATCCAACACCTTCTGCAGCAATGTTTGAGACATTGATTAAATCAGCTGCTAGTTTGAATGTACCTATTGATATATCAAGTGGAAAAAATCTTCAGAATTCTCTGGATGCTGCAGTCTTTGAAGATGATCcttacaaaaatAGAAATTTTCTGACTACCAACATTATGGTCTCGCTACCCCTATTTATACGACATTTTACTTCTCCAATTCGAAGATATCCTGATGTGATGGTTCATCGTTTGCTTGCTGTAGCATGCGGAGCTTATCAGTCAAGTTCAGATTTGCTGAATAAAACAACCGTACAGgcaaTAACTTCGCATATGAATCATCGCCATAAAATGGCGCAGTACGCTGCTAGAGCATCTATCAATTTACATACTCAAatatatttcaaaaatagaaTTTGCGACGAAATTGGctatgttttgtttgtaagaaaaaatgcACTTCAGATACTTATACCTAAATACGGACTTGAAGGCACCGTATACCTATCAGCTAGTAAAGATACAGAGAGTCCCTTTAAGTTTGATGAGgaggCGCTTTCTCAAACTTTGGGAAATATAACGATCAAGGTTTTCGATAAAGTCATAGTTCAAGTTAgtatagaaaagaaaactatCCAGACTTCCGAAATGCAACTGAAGCTGGTTCGTCCCGAGattccTGGTTTGTCGGTACCTGCAGTTggcaatatcaaaaaaattgcaaatgaaGAACCTGTCACAAAAAAGCTTCGTGTATCATAA

Transcript

BRAKERKRET00000001427

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9CSH3	Exosome complex exonuclease RRP44 OS=Mus musculus OX=10090 GN=Dis3 PE=1 SV=4
Q9Y2L1	Exosome complex exonuclease RRP44 OS=Homo sapiens OX=9606 GN=DIS3 PE=1 SV=2
Q9SHL7	Exosome complex exonuclease RRP44 homolog A OS=Arabidopsis thaliana OX=3702 GN=RRP44A PE=2 SV=2

Gene family

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

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17849 all species →	OB_Dis3	Dis3-like cold-shock domain 2 (CSD2)	Domain	Interproscan
PF17215 all species →	Rrp44_S1	S1 domain	Domain	Interproscan
PF17216 all species →	Rrp44_CSD1	Rrp44-like cold shock domain	Domain	Interproscan
PF00773 all species →	RNB	RNB domain	Domain	Interproscan
PF13638 all species →	PIN_4	PIN domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001900 all species →	Domain	Ribonuclease II/R	Interproscan
IPR041505 all species →	Domain	Dis3-like cold-shock domain 2	Interproscan
IPR033770 all species →	Domain	Exosome complex exonuclease RRP44, S1 domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR033771 all species →	Domain	Rrp44-like cold shock domain	Interproscan
IPR050180 all species →	Family	RNR Ribonuclease	Interproscan
IPR002716 all species →	Domain	PIN domain	Interproscan
IPR029060 all species →	Homologous_superfamily	PIN-like domain superfamily	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:0000175 all species →	Molecular Function	3'-5'-RNA exonuclease activity	Interproscan
GO:0000176 all species →	Cellular Component	nuclear exosome (RNase complex)	Interproscan
GO:0000177 all species →	Cellular Component	cytoplasmic exosome (RNase complex)	Interproscan
GO:0004519 all species →	Molecular Function	endonuclease activity	Interproscan
GO:0016075 all species →	Biological Process	rRNA catabolic 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
K12585	DIS3, RRP44; exosome complex exonuclease DIS3/RRP44	EC:3.1.13.-	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 BRAKERKREP00000001427.1 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

24TPM > 0

7Conditions

1,404.6Max TPM

538.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	14	615.22	1,404.58
Whole	6	6	532.32	555.29
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	381.83	381.83
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	393.53	393.53
symbioic hydra M9 strain · symbioic hydra rep1	1	1	327.65	327.65
symbioic hydra M9 strain · symbioic hydra rep2	1	1	258.18	258.18
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
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	1,404.58
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	1,311.19
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	1,272.85
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	1,254.31
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	1,196.57
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	1,160.75
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	545.34
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	504.76
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	488.17
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	434.39
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	422.07
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	420.74
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	386.67
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	271.50
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
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	555.29
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	554.68
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	536.95
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	536.93
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	528.42
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	481.64
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	381.83
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	393.53
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	327.65
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	258.18
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.