Gene detail

Detailed information of BRAKERKREP00000019862.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047123479.1, lysine-specific demethylase 5A isoform X1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000019862

atgtttccCAATTCAAACGATACAGAGTTTATTCAACCCCCAGAAGCTCCTGTTTTTGAACCAGATGAAGAAGAATGGAAAGATCCTCTTGGATTTATAGCAAAAATATACCCATATGTTGTTAAAGTTGGCATATGCAAAATTAGACCTCCGCCGGATTGGCAACCTACCTTCTCTGTTGATGTTGAAAAATTTCGTTTTACGCCTAGAATTCAAAAACTTCATGAGCTCGAGgcAAAAACCCGTGTCAAGCTTAACTTTATTGACACTATAGCAAAGTTCTGGGAATTGCAGGGATCGTCAGTAAAACTTCCAAATATTGAGAAAAAGCCATTAGATTTACATGAGCTGCACAAGattgtTCAAGCAGAAGGTGGTTATGAAGATGTAACTCGATTGCGTCGATGGAGTCGTGTTGCCTTGCTGATGGGTTACTCTGGCCCTCAGGCTAGTGCAATCTTGAGACgccattatgaaaaaatactataTCCTTATGATGTTTTTATGTCTGGTGCCATGATAGGGGAAAGTaacccAACACAAAGTGCATTTAAAGAAAGGTTTGAGgtgaataaaaacaatgacaaTGGTGACTATAATCAATCTTATAGCTCGCGTCATACTCGTCaatcaaagtataaaaatgatttggtGGATGATATCCCTGAAGTTAATTTTGAGACAAACACAGAGTTAAAAAGACTACAATTTTTGGCACCTGGTCCTAAAATAACTGGTTCAAAACCTGCAGGTCGAACAAAACGTCGCAACAAGAAATATGAAGACCATTTTGTTGAAGATAGTGAACTTTGCGCAATTCAAGGAGTCCAAAATCCTGTTTATCAAAGCaatgataaaaacatatttagtGTAGTTGCATCATGGCAGGGGATTCAAGACTACAGATGCTGTATTTGTGAATGTGGAGATGAGGAGCATTGCATGCTACTGTGTGATGCTTGTGATTCATCATATCATACATTTTGCTTGATCCCTCCTCTTCAAAGTGTTCCACCTGGTGATTGGAGATGCCCAAAATGTGTAGCAAagGAATGTAACAAACCCACTGAAGCCTTTGGATTTGAACAAGCCAAAAAAGAATATTCTTTGCAAAGTTTTGGTGAAATGGCAGATAAATTCAAGGAAGAGTATTTCTCAATGCCTCCCCatgAAGTACCATTACATATTGTGGAGAAAGAATTTTGGAGACTTGTACATTCGATTGATGACAATCTTACTGTAGAGTATGGAGCTGATTTGCACACAAAAGAACTTGGATCAGGCTTTCCACTACCAAATAATACAGATGATCCTGAAGatcaaCCTTACATTGATTCCCCATGGAATTTGAATAACTTAGCTAATAATGATAAGTCTGTGCTAAAGTTTATCACTCAAGACATCTCTGGAATgaagGTGCCTTGGTTGTACATCGGCATGTGTTTCTCAAGTTTTTGCTGGCACACAGAAGACCATTGGAGTTATTCTATTAATTACTGTCACTGGGGAGAACCTAAAACATGGTATGGAGTCCCTGCTAGTGAAGCTGAAAAATTAGAGAGTTGTGTAAAAAGTATTGCACCTGAGTTGTTTGAGAAAAGTCCTGACTTATTTCATCACTTAGTAACAACTTTTTCCCCAATGACGCTGATGAATTATGGAGTACCTGTATTTCGAACAGATCAGCATGCTGGAGAGTTTGTTATTACATTTCCTAGAGCTTATCATGCTGGTTTTAACCAAGGTTATAATTGTGCAGAGGCTGTAAATTTTTGTCCTGCAGACTGgCTTTCAATTGGATTTGATTGTATCGAGCACTACCGAAAATTGCAACGAGCTGTAGTATTCTCTCATGAGGAACTTGTCTGTAAAATGGCATCAGTTCCAGAAGCATTAGACCttgaaattgcaaaaaaattgtatgatAATATGAAATTATTGGTTGATATTGAGTTGTCTGAAAGAGCGGCTCTCCATGAAAAGggtaTAAAAGATAGTGAGTTTTGTCCCTATGAGCTTATCTCAGATGATGAGCGCCAGTGTGATTTTTGCAAGtgtacaatatatttttctgctGTAATATGCTCATGCGATAGCAagCGTTTATCTTGTCTAAAGCATGCAGATGAACTATGTGTTTGTCAAAACATCAGAAAGTATATCCGGTATCGATATACTTTAACTGAACTCCCAGAGAtgttaaacaacttaaaaaaacgaGCTGACTCTTTTGACAATTGGGAGAAGCAAGTGCAAAAAATCTTGTCTTGTTCATCCCAGGATAGATATGATATCTCAGCTTTTAAAGAGCTTATATATGAATCTGAGCAAAGTCATTATCCTGACTGCGAACTTCTTGAGCAACTTAAGTCAACTGTTGTTGAAGCAGAGCAATGCTCACAAGTTGCAAATCagtttattgcaaaaaaacacaaaactagAAAATCCAGCAGCATCTCATCTGTACAATTACCTCGTCTAACCCTGGAAGAACTTAATGATTTTGTTCTTCAAGTAAAAAATCTACCGTGTATTATTAAAGAAGCTAAAGCAATTGATATACTTATGTCACAAATTGATACTTTTCGACATGAAGCTCGTCTTGTTTTGAATTCAGACAAGTACAATGAGCAAAAGGTTTCTGAATTGATAGAACACGGCAATTCGATGGATGTTGAATTGCCAGAAATGCATGAGTTAAAAATGGATCTGAAGGCTTCAAAATGGCTTGGAGAAATAGTCCAATTGCTAAACCAAGAAGAGCCCATTTCACTTGATGTTATCCGAACATGTGTTGATCAAGGGATtggacttaaaaaaaagccagTTTCAACTGAACCGTTATCTCAACttaaagaattattatttGCTGCTGATCGATGGGAAGAAAAAGCTAAACTCTGCCTGCAGGCCAAgCCTCGACACATGATTGGCACATTAGAAGTAATTGTACAAGAAGcctcaaaagttaaaattcttCTGCCAAATGTATCAGCATTAAAAGATGCTCTTGTTAAAGCAAAAGAATGGACATCAGAAGTTGAACGAATGCAGAGCGATGACTATTATCCCTATTACGATGTATTAGATGCCCTAGTCACTAACGGTAGACCTATTCCAGTTCGCTTAGAACAATTATCCCAAATGGAATCACAGGTTGCTGCTGCCCGTGCCTGGAAAGAACGTACCTCTAGGATATTCCTGAAAAAAGGATCAGAGAAAAATTTGCTTGAGGTCCTTAGACCTCGTAAAGATGTTGGagtgtttgaaaataaacaaaaaatagagaaaaaaaatgatgattcaGAAAAGTGCAAGAAACACgaagaaaagacaaaaaaattaaacgagaagaaaaaagataaaattgatACTAAAGATGAGATTGAAATAAAGTGCGAGGACACCAGGAATGGAGCTGAAGGGAGTCGTTACTCAATCGATGATTACTCATCGTATGACCCAGTTGCTGTTGCACAAGCGTTAAAACTTGCggaaagaaatgaaattgaagctattaaattaattagaGCTAAAAATAGAGATAAGTTAAGTACTGAAAACATAGAAGGTCCTTATTGCTTATGTCGGAAACCTATAGAAGGTCTTATGGTCCCTTGTTCGCTTTGTTTAGAATGGTACCACACAACCTGTATTGTTGCTCCTAAAACTATATACGGTAGGCCTATTGGAAAAGGGTTTACTGCGTGGTCTGTATCGCGTGAAGTTCATTACCTGTGCCCTGGATGCTGCCGTACCCGTCGCCCACGTATTGATGCAATATTATCTCTTCTTATGTCATTACAGAAACTTCCAGTGCGTATTGCCGAAGGAGAGGCACTTCAATTTCTCACAGAACGTGCAATGAATTGGCAGGATCGTACTAAAATAGCTTTATCCCATCCTGAGATTCAGCGTATCAGCGATTGTGTAAAACGTGATATTGAACAAACTGAGAAGCAAGTCACACACttgctttttttacaaagactaCTTACTgtacaaaaagtaatttacattaaaaacgAGAATCAGTTAAAGGAGGAGAACGAACTTGAATTGAGAGAACGATTGTCTATTAAAACTGAGCCAATAGATATTAATTCGCCAGCTGCGCAATCATTTGAAACTAAAGCTTTCTTTGCAGAGCCAGGACTTGAATGCACAGAAGAAATGTGTAACGGTAGTCCGGGCTCTAAGGAAACTTTTAAATCCTCTTTCTCCAACCCTGATATTGTTCGAGTTCAAAGCGCAAATTCGTCACGTGCGCAAAGTCCTATTGATGTTTGTGTTCCACTTGTCGAGCGAAAAATGCTCACGATGCAACCACTGCCTAACTTTGTCTTGGACGAACTTGAGGTACTACTATACGAAGGTAGTGTTCTCGAAGTTGGATTAGACGAAGTACAGATCATATGGGCTATATTGCAGGTTCAAAAGCCGCTCTTGAAAGAGGATTGCATGATAATGAATGCAGATTATCGTCGCAGTCtagcaaaaaacttaaagaaacaGAGGAAACGGAAGCTTGAAGAGTCAAAGCACGCAAGTAAAGCAGTTACTTTACCCATGATCGATTGTGCTGCCGTAAAGAAGCTAAAAGAGATTGTTTCGCATCGTAAGAAGGATGAAAAAGCCGAAAAGATTCGCTCTCCCATAGTAGAGAAAGAAGACGAACAAGATGAAGATGACTGCTCTGCAAAACCTTGCTTGAAACCTTTAGGCGAAGAAGTTGAGTGGGTACAATGTGACGCTTGTGAGAGTTGGTACCATTGCGCTTGTGTTAAGATAAGTGCTCAAGAAGCAACTAATGCAGACGAGTACAAATGCCCTTATTGTAAAACAGAGACAAATGAACAAGATGCGCCTAGTCTCAACATTATCGCAGAGTTGGCCCATCAACTAATTAAAGATGCTCctgtaaataataatgatttagAGAATGGGACTTCAGACAACAACATTTCTTTAAGTTCACATATATCTGGGTTAGatagtttgttttgtttggccGATGCAAGTCAAACTATGGATACTGCGCCATTATGTATTATGTCTTCGGAAACAGCTTCTGTATGGAACTATTCCAAAGAGATAGCGCCGCGTGTTGAACTTGTAATGGAATAA

Transcript

BRAKERKRET00000019862

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3UXZ9	Lysine-specific demethylase 5A OS=Mus musculus OX=10090 GN=Kdm5a PE=1 SV=2
P29375	Lysine-specific demethylase 5A OS=Homo sapiens OX=9606 GN=KDM5A PE=1 SV=3
P41229	Lysine-specific demethylase 5C OS=Homo sapiens OX=9606 GN=KDM5C PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004250 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02928 all species →	zf-C5HC2	C5HC2 zinc finger	Domain	Interproscan
PF02373 all species →	JmjC	JmjC domain, hydroxylase	Domain	Interproscan
PF01388 all species →	ARID	ARID/BRIGHT DNA binding domain	Domain	Interproscan
PF00628 all species →	PHD	PHD-finger	Domain	Interproscan
PF02375 all species →	JmjN	jmjN domain	Family	Interproscan
PF08429 all species →	PLU-1	PLU-1-like protein	Family	Interproscan
PF21323 all species →	KDM5_C-hel	Lysine-specific demethylase 5, C-terminal helical domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036431 all species →	Homologous_superfamily	ARID DNA-binding domain superfamily	Interproscan
IPR019786 all species →	Conserved_site	Zinc finger, PHD-type, conserved site	Interproscan
IPR001965 all species →	Domain	Zinc finger, PHD-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR004198 all species →	Domain	Zinc finger, C5HC2-type	Interproscan
IPR003347 all species →	Domain	JmjC domain	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR001606 all species →	Domain	ARID DNA-binding domain	Interproscan
IPR019787 all species →	Domain	Zinc finger, PHD-finger	Interproscan
IPR003349 all species →	Domain	JmjN domain	Interproscan
IPR013637 all species →	Domain	Lysine-specific demethylase-like domain	Interproscan
IPR048615 all species →	Domain	Lysine-specific demethylase 5, C-terminal helical domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10694 all species →	LYSINE-SPECIFIC DEMETHYLASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0010468 all species →	Biological Process	regulation of gene expression	Interproscan
GO:0032452 all species →	Molecular Function	histone demethylase activity	Interproscan
GO:0034647 all species →	Molecular Function	histone H3K4me/H3K4me2/H3K4me3 demethylase 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K11446	KDM5, JARID1; [histone H3]-trimethyl-L-lysine4 demethylase	EC:1.14.11.67	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 BRAKERKREP00000019862.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.