Gene detail

Detailed information of BRAKERKREP00000015799.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047125290.1, uncharacterized protein LOC100204596 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000015799

ATGTCTGAGCCGGAATCACCAGATTGTCCACTATGTATGGAACTGCTTGAGATAGATGATCTTCATTTCTATCCTTGCACTTGTGGCTATCAGATTTGTAGATTTTGTTGGCATAGAATAAAAACAGATGGAAATGGTTTGTGCCCTGCTTGTCGTAAAACCTATACTGAAGACCCAGCCATGTACCGTCCGCTTTCTCAAGATGAAATTCAGAAAGCTAAGAAAGAAAGGAAGCAGGTAGAGACACAGCGGAAACAGAAGGTCACTGATACAAGACAACATCTTTCTGATATTCGCGTTATTCAAAAGCatcttgtttttgttgttggatTGTCGAAAAAAATGGCAGATGCAGAggtttTAAAACAGCATGAGTACTTTGGAAAATATGggaaaatagttaaaattgttataaatccAAATACAAATTATGCTGGACCTCAGGGTCCAAGTGCTAGTGCATATATTACCTATACTAAAGTTGAGgatgCCCTTAAAGCAATACTTTCTATCAACAGTATGCAACCtcctttaaaaataagggcATCCCTGGGAACTACTAAGTATTGTACTCATTATCTTCGAAGTATGCAATGTCCAAAGCAAGACTGCATGTATCTTCATGATGTGGGAGAAGAAGCAGCCAGTTTTACTAAAGAAGATATGCAGGCTGgAAAGCAccagatttttgaaaaaaatctccttGAGAACTATGCTGCTAGAGTGCGTCAGCAGCAGCAAATACCAAACagcaataaacaatatttggaGGAAGAGAATATTGAACCATCTTCTCTTGATAATTGGGGAGACGATATGGAAAATGCAGATTCATTATTGCCTTCTCAAGCATCTTGGGGGACTTCAAAAGATGACCGTTGCGATAGTTGTCcaaaagatttagaaaataaaaatgatcagCCAGAATCTTCCAAATTCCAAAAGAGTTTAAGTGAAGTTGGACAGTCAAGCTTGCGCTCTTCAAATGAAGATTTCTCTTTATCTCAACAAAACAAATGTGACTCATTGACTCCAGAATTCTCAACAGGTTGGGCAACATCTGTTGAAACTGCTCCAAATGAGCCATTACAATCAGCTGATGAAATAATAACAAGCAGTTTTACAATGTGGCCTGGCATGCTTGACCTTGGTCTCAGTGATCTCAAGATAAATTCTTTTGATGATGAATTAGgttttgatCCATTCAGAGAAAGTACTTCTGGATTAGAAGATTTAATTGCTATTGAAAAACAACAGGGTCTAAATCCTCCTCCTCAACCTTCATTTACATGGGATTCATTTTGGCCATCTTCTTTTtcatctaatttaaaaaataatgtatctGGAAACTCATATTCTTTATTTGGCAATAGTCAACAACAAGTTTTACCACCTCGACCTTCTTCCCAAGTGATTAATTCTTTTCAGCAACCAATGTCATCAACAACTCTTAATCCTGTATGTAATCCATCTCCACTTCGCTTTATTTCTCCTCAGCAAATGCAACCTCATGGTTTTTATTCATCTTTTCCCCATATGCAGCAGCAACAGAGTCATGAAGCTATGAACCAGGTTCGTTTTCAAAGGCTACATTCACAACAGTCTAATTTAGTATCACAACCACCACTAAACATTACACCTTTAGCCAATGCTCCAACAGAAAATAAGAATTGGCAAGATGGCTTGCGTGCATTACttccaaatataaatatcagtTTTGGAAactCTATTTGTAATGAAGCAGAGAAAACAGTTAGTACTTTGGTATCATCGGCTTATGTTCATGGAAACACACCAATTCCACAATCACTATGGATGAATTCAAGCAGTACACGTCTTCCACCTCCACCTGGTTTCTCTGGGTCTAATCCTCCATTTCAAGCTATACCTCAACCTGCTTCTACTTTGTTGAGTATGACATCAACTGGTCAAGGTCCCGTTCTACAAAATACTGGCATTAATTCAAATCTTACTTCTGGATCAACATCTCTTCCTTTCAACAACTTAGCAGCTGTGACACAAAATGAAGATCCTAGTATTTTGTGGTCAAAAGTGCTCTCTGATGAGAGTAAGGAAGTTAATGCAGTCAATATGGCTTTTCCTTTGCCAGGAGAAAATGTAAACCAGGGTTCTACAAACAATTTACAGCAGCAAAATCACCAGCCTCAACAGGGAATGGCATCGTGGAATATTGTTGTCAGCGGAAACCAACcatcaaaaagtaaacaagaCGACATTATAGTGAAACACCATCAACAACAACCACTGCAAATATCCGCAAAAGAATCCTCTGTTGAGCCGTTAAAACTACAAAAGTCATCACCTATTTTTGGAAATCAAGTCAAAGCTACAGCAAAGAAGCCAACAGCGCACGTTAAACCTCTTAAGTCCAGCATACTCTCAGACGGCTTTACCACCGTCAGTGGATCAAGGCAGCTACCTGTGGGACAACAGCTATCTGTTTATGCTAATCCCTCTTCACGTGTCAGTGAACTTGATGATTTTAGCAACGACTTTCCATCAATTACTAACGGGGGAGGTTTAAGTCTTAGTGATTATACAACAGCAGTCGGTGTTcattcaaaacaacaaaataaaaagaaaaaaaagaaaagtaaagatggttttgaacaaatttctacgGTTTTAGTCAGCCGAGTTGAAACAGACACAACGGAGTTGACTGATGATGAACGTCTTAAAAAAGCTGCTAAGAATAagaagaaaggaaaaaattctCCTCCTTCGATACGAAAATCTCCTCCGACTGTTCAGAAAATAAAGAGTACTCCAAAAAACCAACctattagaattttaaaaagtgatgcTGGCACAACATCCACGATACTGCATTCCCCGACTCAGGTGATAGCTGATCAAGGTGGAGTCGCTTGTAAACCAACCTCGTCTTCTCAGGAACAAGAAATAGTTAGCCGACTAACAGAATCCACTGAGAAACTGCTAAAAAATGTGCTCTTTGAGACAGAAGCTATTAAGCTCAACACCGAGCAGATCTCGAAGGATCTTAAAAGTGCTTTGGAAAAATGCAAGgagtCCTCGTTGTCACTTTCTGACTTAGAGAAAATCAATTTGCTGCTAAGTCCCGGAAAGATTGTGCCCTGTGGATTTGACGATGATTTGCAAGACACATCATTTTTAGAGAGACAAGTTGAGTCTGCAAGGCGAGAAGCAAAAATGCTAGAAGCTCgtttaaatgaagttattcGAAAGAACATGGCAAGTGAATTAGAAGCACTTAAGAGAAATACGAAGcagtaa

Transcript

BRAKERKRET00000015799

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O95628	CCR4-NOT transcription complex subunit 4 OS=Homo sapiens OX=9606 GN=CNOT4 PE=1 SV=3
Q8BT14	CCR4-NOT transcription complex subunit 4 OS=Mus musculus OX=10090 GN=Cnot4 PE=1 SV=2
Q09818	Putative general negative regulator of transcription C16C9.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC16C9.04c PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003643 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14570 all species →	zf-RING_4	RING/Ubox like zinc-binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039515 all species →	Domain	NOT4, modified RING finger, HC subclass (C4C4-type)	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR003954 all species →	Domain	RNA recognition motif domain, eukaryote	Interproscan
IPR039780 all species →	Family	CCR4-NOT transcription complex subunit 4	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR034261 all species →	Domain	CNOT4, RNA recognition motif	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12603 all species →	CCR4-NOT TRANSCRIPTION COMPLEX RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0030014 all species →	Cellular Component	CCR4-NOT complex	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	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
K10643	CNOT4, NOT4, MOT2; CCR4-NOT transcription complex subunit 4	EC:2.3.2.27	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000015799.1 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

11TPM > 0

7Conditions

12.6Max TPM

1.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	2	0.13	1.23
Whole	6	6	6.20	12.59
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	1.22	1.22
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.75	0.75
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.16	0.16
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
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	1.23
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	1.07
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
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
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	12.59
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	9.92
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	4.41
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	4.06
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	3.54
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	2.70
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	1.22
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.75
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.16
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.