Gene detail

Detailed information of BRAKERKREP00000012228.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047133014.1, paired amphipathic helix protein Sin3a-like [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000012228

atgaaaCGAAGCCATGATGAGTCAGATATCTATAGTGTAAGAAGATCAGCCATGTCTGGGTCACACAATCATACTAATATTTCAGGTTCACATCAGAATGCTGTTCTAGTTGGATCACATCCTGCTCCAGGAATTGCTGGTTCTCATCAGTTGCCTGGACCTCATCATCTTCCTACTATATCAGGACCTCACCCTCCTGGAATAAGTGGTGCACACTCTACTTCAGCTATATCTGGTTTTTCTCATCAAGCTCTTGCTCCTACTCCCAAACAGTTGGCACACAATTTTGAGCAAATGAGAGATTTACCAAGACAACCATTTTCAGCACCTCATATGCCTGTACCTAATGCttcaaactCTTCCCCACCAGTGAATGGAGCTCATTCTTCATTGTCTCAACCATCTGCACATATCCCATCAAAGCCTTCTTTTCAAACGCATATTCAAGGTCCTTCTCACATAACTGCTGGAGGACAACAGCAGTACCAGAGATTGAAGGTTGAAGATGCATTATCGTATTTAGACCAAGTAAAGCTACAGTTTGGAAGTAAACCTCaagTCTACAATGAATTTTTGGATATCATGAAAGAATTCAAATCACAAACTATTGATACACCTGGAGTAATCAGTCGTGTTTCAGCACTTTTTAAAGGACATCTGGATTTGATTGTTGGctttaacacatttttaccCCCTGGATACAAGATTGAAGTAAGTTTAACCGATATTAACACTGTGAATGTGTGTGCACCAACAGGTACTACAACCCATCTTATTTCAGGAAGTGGACTTATTGCAGCTCCCAGTCAACCAGTTCAGAATAAGCCACCTATTGTACCATCTATAAGTCAAGTAAGTACACTGGTATCTACTGCTGTAACTACTACATTACCAAAATCTCCAACTCGGCCAACTTCATTGCCATCAAAGACTTCTTGTTCCCCGATTTCATCCGCTCCTGTTATATCTTTACCTTCTCCTGGTGTTCAGTCTCAAACACAGGCTCAACATCATGCAATTAACtatgtaacaaaaataaagaatcgGTTTCAAGGTCAACCTGAGGTCTACCAAAAGTTCCTTGACATTCTGAATAACTATCAAACAGAGCAGAAAGCAATTAAAGAGAACACTGTTGATCAATATGGTAGGGTGTGTCAAGAGCAAGACATTTATGCTAGAGAAGGTAAACTTGCTACTGAGGTGTATCAGCAGGTTGCCAAACTCTTCAACAAGCAAGAAGATTTGCTTCAAGAGTTTAGTCAATTTTTACCAGATGCTACCGGGTCAACATTTAATCCCAATATGGTATCAACTGTTGCTGCTGCCACCGTGGTTACCCAGTATCAACCTTTATCTAAAGGCACCAAAATAACCACATCAGCAGGAAATAATGCAACAAAAATTCTAACAGCtaagacaaaaaagttaagcTCTCAAAATACGGTTAAGCAAGAACAAATTGAGGTTGATAAAGatatttctgataaaaataaaaaacgccATAAATCAGCATTAAAAGACATTTCCCTTGAGGAGGCTGTAAAGCATGGCAGTTTTAGtgattttgcattttttgataaagtgagaaaagcattaaaaagtcAAGAAGtctatgaaaattttcttcggtgcttaatattatttaatcatGAGGTTATTTCTAGGGCAGAATTAATTCAACTTTCTACAACATTTTTGGGAAAATTCCCTGATTTGTTTAATTGGTTTAAAGCATTTCTTGGATATAAAGATAATCAGCAAACTGAAACAAATATAACAGGATTTAAGGACAGAGGAACTGGTGGAGAATTGGCTCATTTAGAGATtgATTTTGCATCATGCAAAAGGAGTGGTGCTAGTTATCGTGCTTTACCTAAAAGTTACATTCAACCAAAGTGTTCAGGTCGAACTCAGCTATGTAAGGATCTTCTAAATGATACCTGGGTCTCACTTCCATCCTGGTCTGAAGATACTCAGTTTCCTGGAACAAGAAAAACACAATATGAAgagtatatttataaatgcGAAGATGAGCGCTTTGAGCTTGACATTGTTGTAGAAGCAAACCTATCTACAATTAAAGTTTTGGAGggtattcaaaaaaaactttcaaggATGAATACTGATGAACAGCAGAAATTACGTCTGGACAATTGCTTGGGAGGTACTTCTGAGATCATCCATAGAAAAGCCATTTACAgaaTTTACGGGGACAAGTCACCAGAAATTATTGATGGTTTGAAGAAAACACCAAATGTTGCAATACCTGTGGTATTAAAACGTCTCAAACAGAAAGATGAGGAATGGAGAATTGCACAGAAGCAATTCAACCGGATATGGAGGGATCAGAATGAAAAATACTAtcttaaaTCATTAGACCATCAAGGTATAAACTTCAAACAAAGCGATTTAAAAGCTATTCGATCAAAAAGTATAATTCGTGATATAGAGCTGTTATATGAAGAGAGAAGTGATCAAATAGACGAGGGCAGCACTGAATTATCTGGACCACACATCACTTTTGTATATCAGGATCAGTCAACACTAGAAGATGCATCCTCATTAATCATTCATCATATGAAGCGTCAAACAAGCATACACAAAgaagacaaaacaaaaattaaagctgTTCTACTTCATTTTTGTCAATACTTGTTTTTTGCACCACCTGGCGATTTAAGTGATGATGAGCAAGATGAAATtccagaaaagaaaaatatatcatatcaAAATGATGaatataacttgttttttacaaatagcACATGGTTCATCATGTTAAGGATGCATCAAatGTTATGTGAGCGGTTGCTGAAGATGAATCAGCTTGCTGCAGAAGCAGCAGCATTTGaatcaaatgataaaaaacacaGAAGAGAGGGGACAGCTATAGCTTTGCGTTTAAAGAAAACACCTATAGCTGATGTTGAAGATTATTATCCAGCGTTTTTGGTCatggttaaaaatttgttggatggaCTTACAGATTCAAATGCATTTGAAGATTCCTTGCGTGAAGCCTTTGGTGTAAACTCATATATTGCATTTACAATAGATAAACTAATTCAGAATATTGTTCGTCAGCTTCACAGCCTTGTAACAGATGATATCAGCATGAAGCTGTATGCTATATATGAGGATGAACGTCGGAATGGTGCTGCAGGTGGCTTATCTATTACTGCAACAGCTAGATCTGCTTTAGAACTAGCCTATCAAAAGAAAGTAGAAAGCATTTTGTCAGAtgaaaattctttcaaaatttattttCACAAGGATAATGGCACATGCAAAGTTAGTATGGAGCTTCTTCCAAATGAAGGTGACTCATCTGAAGATCAAGCTGAAGTTGagAGTCACCATATCTACAACCTTCCATTGTCTGAGAATAATGCAAATTGTGACTTATCAGAGAACATGATGGAGTTCCAAAATGTCATAGTTCTCTCCACCATTTCATGA

Transcript

BRAKERKRET00000012228

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q60520	Paired amphipathic helix protein Sin3a OS=Mus musculus OX=10090 GN=Sin3a PE=1 SV=3
Q96ST3	Paired amphipathic helix protein Sin3a OS=Homo sapiens OX=9606 GN=SIN3A PE=1 SV=2
Q62141	Paired amphipathic helix protein Sin3b OS=Mus musculus OX=10090 GN=Sin3b PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003099 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08295 all species →	Sin3_corepress	Sin3 family co-repressor	Domain	Interproscan
PF02671 all species →	PAH	Paired amphipathic helix repeat	Repeat	Interproscan
PF16879 all species →	Sin3a_C	C-terminal domain of Sin3a protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013194 all species →	Domain	Histone deacetylase interacting domain	Interproscan
IPR003822 all species →	Repeat	Paired amphipathic helix	Interproscan
IPR036600 all species →	Homologous_superfamily	Paired amphipathic helix superfamily	Interproscan
IPR039774 all species →	Family	Transcriptional regulatory protein Sin3-like	Interproscan
IPR031693 all species →	Domain	Sin3, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12346 all species →	SIN3B-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000118 all species →	Cellular Component	histone deacetylase complex	Interproscan
GO:0000122 all species →	Biological Process	negative regulation of transcription by RNA polymerase II	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0003714 all species →	Molecular Function	transcription corepressor activity	Interproscan
GO:0016580 all species →	Cellular Component	obsolete Sin3 complex	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
K11644	SIN3A; paired amphipathic helix protein Sin3a	-	Chromosome and associated proteins	ko03036	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000012228.1 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

6TPM > 0

7Conditions

3.9Max TPM

0.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	0	0.00	0.00
Whole	6	4	2.09	3.88
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	3.03	3.03
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	1.45	1.45
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
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	3.88
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	3.49
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	3.04
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	2.15
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	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	3.03
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	1.45
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.