Gene detail

Detailed information of BRAKERKREP00000025344.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047136617.1, E3 ubiquitin-protein ligase SHPRH-like isoform X4 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000025344

ATGAATGTTCATCGTTTGTTGATTCAACAACATTATGAGGAAGAACTTACGGGTGctgaaatattcaaattagTAAAGGTACATGGAATTAATGAGAGATGTGTTTATCGAACTATCCAACAGTTGCATGAAACTGGTGGTGTTGAAGACCGTGAAAGtaaccTGGCAGTTCAAATTTCAGCTACTCAACCTACATCAGGCCAACTGTCAATTATATTGAATGTAGGCAAAACGGTTGAGGTTTTAGCATGTATCTTGAATAACCAATGTCCGATTAAGTACTCATATGATAGCATAAAAAGCATATGTAAAGAAGAAGACAGTTTTGATGTTATCAGAAATAGCAATACTAAGAAATGCAACGTAAATGTTGAGGTAGCTACAAGCGATACTGAAAATGTAATCTCAGATGGTATTTTTATGTCCTCCAAAAATGATAGTTGGTTACCATCtcctgttaaaaaaacaaaattttacaaaaacttatttgattCATGTGAAGTTGAGAATGAACAgactttaaatttagataaaaagtatttatttctgGAATCTGCTGTGTGTGATATATGTGGGCATACAAACAATtatgaattattaaatataaaagttaaatgtgAAGAGTGTGACAGTGTcatgcataaaaaatgttcaggCTTTACGGATTTGAATGTAATAGACTATCTCTGTCCAACTTGTGCAATCAAACAGgTTATAGAGACACACTGCACACTTATAGTGTGTCCAGACACATTGGTAACACAATGGATTCTAGAAATTGAGAAACATGTGAAGAAAAATTCTCTAAAGTATATGgtTTACAAAGGTGTAAAACATCACCAGTTTCTTCAGCCAAAATTCCTTGCAAAGTATGACataattttaacttcatttagCACACTTCGACTGGATTTCAACTATGTTATGGCTGATAATGCAAACAGATCTTTACGCCACAAGAAAAAGTATGTCATTTTACCATGTCCATtgattggtttaaaattttggagAATTTGTATAGATGAAGCTCAAATGGTAGAGTGTAAAGGTACAAAATTAGTAGAAATGTCACTTCGAATCAGTGCACATCATCGATGGTGTGTTACTGGAACACCTgtgcaaaagaaaattgaagATATATATGGTCTTTTAATGTTCTTATGTGTGAAGCCATATGGCTCACAAGTTTGGTGGAAAAGAGCATTGCATGATTATTACAGAGCTGGCGATcatcaaaaactctttaaccTTGTTGCATCAGTTACTTGGAGAAATAGCAAAGTGCATGTAGATTCGCAGTTAGGCATACCTAAGATGACTGAGTTTTTAACAACTCTACATTTTTCTGCTAtagaacataatttttatttcaaagaacATGAGAAATGTCAGAGGAGAATTGATTCAAAAACAGggttaaaagaattaaatcaATCTGTTAAGTTGTCAGAGTTGGTTCAAGAATCTGTTAATCagattttatcaataatgCTTCCCCTGCGTCAAGCATGTTGTCACCCATCTGTTgtcagaaacaattttttttttgttgaaaaaaataatattactatggataaacttgttaaaaagcTAACTTCTGATGCAAAGGTTGAATCTGAAGAAGCACATCGAAAATTGATTTGTGCCATAAATGGCATAGCTGGGGTTGAGATCCTTATGGATAATATTCATGCTGCAATTGAGTTTTATGAACAAGCAATATCTTCATGGAAGAAGCATTCAGATCTTCATACTGACTCATTGCAAaaattgCACACTCTATTTAATCTTCATGAAATTCTGGTATCATTTGAATCAAGCAAGTATAATGAACAAAGCTTGATTGAAATGCTTCATGAAATTGAAGATATGCGCTTTAGATATCTGACTCCTATAAGAAATGATATTGAAGCAAGCAAAAAAGAGCTGGACCAAGTTAAGATGGACATCAATGAAAAGAGAAACaagatTGATTTTGAGAATCCTTGGTTCAGCTCTTTGTCTAGTTTAATGGATATtgtccaaaaaaatattgaccaATTAGAAttaactCGTAAACAGATATACATTGAACTgaataatattgtaaaatttccAGAAGTATCTTGTATAAGGGAGGCAGCTGAGTGTTGTTTACGAGGCAGCAAAAGTGTGGGACTAGGAAGACATACATGGTGCTTGACAGAAAATAGTGTTATTGTGTCATTTGCTGAGCCAAAAATAgatgatgaagaaaaaatcattaatgaTACAGGAACTGAGGGAGAATGTCAATCCAGAGGATATATCTTCTTTGATGTAACCAATCATAGATGA

Transcript

BRAKERKRET00000025344

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7TPQ3	E3 ubiquitin-protein ligase SHPRH OS=Mus musculus OX=10090 GN=Shprh PE=1 SV=1
Q149N8	E3 ubiquitin-protein ligase SHPRH OS=Homo sapiens OX=9606 GN=SHPRH PE=1 SV=2
Q9UTL9	Uncharacterized ATP-dependent helicase C144.05 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC144.05 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003108 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00176 all species →	SNF2-rel_dom	SNF2-related domain	Domain	Interproscan
PF21325 all species →	SHPRH_helical-1st	E3 ubiquitin-protein ligase SHPRH, first helical domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000330 all species →	Domain	SNF2, N-terminal	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR052583 all species →	Family	ATP-dependent Helicase/E3 Ubiquitin Ligase	Interproscan
IPR048686 all species →	Domain	E3 ubiquitin-protein ligase SHPRH, first helical domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR019787 all species →	Domain	Zinc finger, PHD-finger	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR038718 all species →	Homologous_superfamily	SNF2-like, N-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45865 all species →	E3 UBIQUITIN-PROTEIN LIGASE SHPRH FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0140658 all species →	Molecular Function	ATP-dependent chromatin remodeler activity	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006974 all species →	Biological Process	DNA damage response	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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

No KEGG orthology assignment for BRAKERKREP00000025344.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000025344.1 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

18TPM > 0

7Conditions

1,138.5Max TPM

294.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	8	247.72	1,138.46
Whole	6	6	331.86	357.64
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	417.24	417.24
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	458.96	458.96
symbioic hydra M9 strain · symbioic hydra rep1	1	1	531.01	531.01
symbioic hydra M9 strain · symbioic hydra rep2	1	1	692.14	692.14
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
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	1,138.46
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	661.26
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	569.76
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	527.66
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	481.10
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	412.34
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	340.92
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	327.42
SRR21134051	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
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
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	357.64
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	354.89
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	336.66
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	321.46
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	321.15
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	299.36
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	417.24
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	458.96
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	531.01
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	692.14
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.