Gene detail

Detailed information of BRAKERKREP00000001204.1 in Hydra viridissima

Genomic Location: QPEY01000003.1:2552358...2567208
NR annotation: XP_002164134.1, histone acetyltransferase KAT6A isoform X1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000001204

ATGACAAAAACTGATCATGCTACTGTTATACCTTGGGTGCTAGCATCTATTGCTAAAGTTAAAGGGCAGAAGCAGCAACCAAATGAAGAAAGAATCTGCCTTGTGTTATTGCAATCTTATGGGCTGAACAAAGAGGAAGGGCTtgaacatcttttaaaatgtgttgAAGAAGGTCATGTTGTTGTTCAAGAAGCTAAAAACGGAAAAAATTCTTATCGAAATGCTAAAGCTGTAGCTGCAGCTGCTATTGGGAAAAAATctccaggtgtgaattattttcaattaaaaaagtgcATAGATGAAGTAATTTCACGTCCACCACGTGAAGAAGGAATTACAATAGAGGAAATCGAAAATGAAATTAGATGCACTAAGACAGATCTTCTAGATTTAGAGCATCCTGACTTCCATCAACAATTTCGACAACTCATTAAAAATGGTATGACAAAACATCGTTATATTAAGGAGggaaaattctataaaatggCTACGTTTTCTTCTATGAAGGCTAAAGTAAATAAGTTATCTGAAGCTGATGTTAAAGAAGGAATAACTCCTGAGGAAAGAGATGCATTAAAAGAGATTTGTGGATTTTGTAAAGGAGATAAATTCAAGAATAAATATGATGAAGAGGAAGATCTTTTAGTTTGTGATGAATGTGGAAATAGtgGGCATCCGTCCTGCATGCAGTATTCAAAAGAACTTACTGCTCGTGTGCAACAAGAACCATGGCAATGTATGGAatgcaaaaaatgtaacatatGTAAAGATCAAGGGGAAGCAGCAAATTTGCTATTCTGTGATGCTTGTGATAAAGGCTATCACATGGCTTGCTTGGACCCTCCTCTTGATGACATGCCAATAGGAACATGGATCTGTGATAACTGCTTGTCAGAAAGAAATGGAAAACGAAGAAGAATATCAAGTTCAGTCCCAGCATCACTCCTTCTTTCAACTCCTGATTTAAAGTCTAAGAGCAAAGGTGCAAATAAACGTAAAGGAGAGAGTTTTGGAAGAGATGAAAGTGATGAAGACACTATaaaaggttgTACTACACCAGGGTGTACTGGTGCTGGACATTCTCTTGGAAAATATGACAGTCATAGATCgGTACAATTCTGTCCTTTGGttcaaagtgaaaaaaaaactagaaaactTGATGCTTTAGATCATGGATATAACCCCCCTCCTCAGCCAAAATTGCCAGgtGTGACAGAGAAAGATGAAGAAATGTTTAGAAATGCTCAAGAAAAAGCCAACTCATATGTGACAACTAATAATGAACCTGTTTCATCAATAAATAATGTAAGATGTCCaccaaaaattgaatttggaAAATATGAAATAGAGACATGGTACTCATCTCCATACCCTCAGGAATATGCTAGTGCTCCTAAACTTTATTTGTGTgagttttgtttaaagtacatgaaaacaagaacaattttaaagagGCACTTGatgaaaTGTCATTGGAGTCATCCTCCagcaaatgaaatttataaaaaagataatctttCAGTGTTTGAAGTTGATGGAGCAGTGAGCAAgATATACTGTCAGAACTTATGTTTGCTGGCTAAACTATTCCTTGATCACAAAACACTCTATTATGATGTTGAACCATTTTTGTTCTATGTATTAACTAAGAATGATAATACTGGAAGCCATCTTGTTGGTTATTTCTCaaaggaAAAGGCTTGTCAACAAAAGTATAATGTTTCTTGCATTATGACTATGCCTCAGTATCAGCGTCAAGGTTACGGCCGCTTTCTCATAGATTTcagTTATTTCTTATCAAGAAAAGAAGGTCAACCTGGATCTCCTGAAAAACCTTTAAGTGATCTTGGGCTAATTACATATCGAAATTACTGGAAATCAGTTATAGCAGAGTATCTACATGAGCGTATGTATGAGAAAGCAGTAACAATTAAAAccatAAGTGAAGCTACAGGTATGGACCCACATGACATAGCAGCAACTCTACAGCAATTAAACGTTGTACAATTACGCAATGGAAAAGTTACTATAGTGATCAATGAGCGCGTGATGAGTGAACACAtggaaaaagttaaacaacaaaaaagaattccAATTGATGAAGAAGCTCTCCGTTGGACTCCTTTAGTTCATTCTAGTACTTCGCAGATCATGAAAGATGAAAATATGTCGTCAGAAGAAGACAACACAGACGgtgataatgataaaaaatcagATGACAATAAAgcagaaaaattattgaacaAATCCAAAATAACTTCGGATGATACTACGAAAGCGCCACTTATTTCAAATACTAATAATGTCGCAGAAAAAGACGGTTCTGCGGCTGAAAAGATAGAGAAGCAagtaaaagaaacaaaaaacattgatCTCAATAATTCTTACTCTGAGTCTTTAGACCATGAATCAAAACCCTCCTTAACAAGCGATCTTATTCATACATCAGATGAGAAACCTCTTACAATTCCTACCGATGAACGCAGCGTTTCCTAA

Transcript

BRAKERKRET00000001204

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5TKR9	Histone acetyltransferase KAT6A OS=Rattus norvegicus OX=10116 GN=Kat6a PE=1 SV=2
Q8BZ21	Histone acetyltransferase KAT6A OS=Mus musculus OX=10090 GN=Kat6a PE=1 SV=2
Q92794	Histone acetyltransferase KAT6A OS=Homo sapiens OX=9606 GN=KAT6A PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000832 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01530 all species →	zf-C2HC	Zinc finger, C2HC type	Family	Interproscan
PF01853 all species →	MOZ_SAS	MOZ/SAS family	Family	Interproscan
PF21524 all species →	SAMD1_WH	SAM domain-containing protein 1, WH domain	Domain	Interproscan
PF17772 all species →	zf-MYST	MYST family zinc finger domain	Domain	Interproscan
PF00628 all species →	PHD	PHD-finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR002515 all species →	Repeat	Zinc finger, C2H2C-type	Interproscan
IPR002717 all species →	Domain	Histone acetyltransferase domain, MYST-type	Interproscan
IPR048589 all species →	Domain	SAM domain-containing protein 1-like, WH domain	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR001965 all species →	Domain	Zinc finger, PHD-type	Interproscan
IPR050603 all species →	Family	MYST family histone acetyltransferases	Interproscan
IPR019787 all species →	Domain	Zinc finger, PHD-finger	Interproscan
IPR040706 all species →	Domain	MYST, zinc finger domain	Interproscan
IPR036060 all species →	Homologous_superfamily	Zinc finger, C2H2C-type superfamily	Interproscan
IPR016181 all species →	Homologous_superfamily	Acyl-CoA N-acyltransferase	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10615 all species →	HISTONE ACETYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0004402 all species →	Molecular Function	histone acetyltransferase activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000790 all species →	Cellular Component	chromatin	Interproscan
GO:0003712 all species →	Molecular Function	transcription coregulator activity	Interproscan
GO:0045892 all species →	Biological Process	negative regulation of DNA-templated transcription	Interproscan
GO:0045944 all species →	Biological Process	positive regulation of transcription by RNA polymerase II	Interproscan
GO:0070776 all species →	Cellular Component	MOZ/MORF histone acetyltransferase 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
K11378	SAS3; histone acetyltransferase SAS3	EC:2.3.1.48	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 BRAKERKREP00000001204.1 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

85.8Max TPM

15.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	3	8.88	85.78
Whole	6	5	29.43	41.40
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	31.90	31.90
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	25.76	25.76
symbioic hydra M9 strain · symbioic hydra rep1	1	1	49.12	49.12
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 the sample table (29 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	85.78
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	41.47
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	32.58
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
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	41.40
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	40.10
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	34.01
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	31.44
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	29.65
SRR10058802	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	31.90
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	25.76
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	49.12
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.

Co-expression network

Genes whose expression across the transcriptome samples of Hydra viridissima tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	15	BRAKERKREP00000001662.1	0.964304352133279
Negatively correlated	4	BRAKERKREP00000024112.1	-0.68571350363575

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Hydra viridissima, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →