Gene detail

Detailed information of BRAKERKREP00000026481.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047134993.1, DNA (cytosine-5)-methyltransferase PliMCI [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000026481

ATGCCCGTtctaattgatgaaaaaaaagaagtttcaaGTCCTGGTGCATGTGGGAGTAGTAAAAGTGATCTGAGAAGTAAGCAATCTACAATTACTgctcttttcaataaaagAGCGAAGAAAACAAAGCGTTCTTTATCTCCtagtaaagaagaaaaaggaaataaaaagaaaaaaactgaggATAACATTACAGAAAGcTCACTTACATTGCGGGAAAAGCCTGATATAAAGaccttagaaaaatgtaaagaatGTAGACAAGTATTGAATAGCGATGATTTAAAGGTGTTCCATGGAGACCACAGTGATGCTTTAGAGGAGTTTGCAATGCTTGTTGATCCCAGATTATCGTTATTGTCTGGAAATGAGCAAGATTTTGATGCTTATGAAGAAAGACCTCAACATAAAGTCACAGAGTTTAGCATTTATGATAAATGTGGTCATCTTTGTGCATTTGACACTGGTCTTATTGAGAAAAATGTTGAGCTGTTTTTCAGTGGTTATGTGAAGCCTATATTTGATGAGAATCCTGATATAGAAGgGGGAATTTGTACAAAAGCTATGGGACCTATTAATGAATGGTGGATTGCTGGTTTTGATGGTGGAGAAAACGCTCTGATCGGTTTTGGAACTGCATTTGCTGAATACATTTTAATGAGACCATCTGATGATTATACTTTGTTCATGAATGCAGTTACTGAAAAGATTTATATGAGCAAAatagttatagaatttcttttaaacaatccTGATTCTGAATATGAAGAACTACTCAATAAGCTTGAGactACAGTCCCACCTGAGAATTGTGCAAAGTTTACTGAAGACACACTGTTGCGACATGCTCAGTTTCTTGTGGAACAGGTTGAGAGTTATGATTCTGCTGCATTGGATGATGAAGATTCTCCACTCTTAATTACATCAAGCAGCATGAGAGACCTAATTAAGCTTGCTGGTGTAACTTTGGGAAAAAGaagaCAAATGCGTGGCCTGAAGGTGAAAGGAGAGAAAAAAGCTCTTGGTCCAACTCTAgCAACAACAACACCTTTGGTACGGCATGTTTTTGATACCttctttaaaaaccaaattgatttaaaaggtGTTACTACACAGCGTAGAAAGCGTTGTGGGATCTGTGATATTTGTCAGCAACCAGATTGTGGAGTGTGCCGTTCTTGTAAGGACATGGTTAAGTTTGGCGGAAGTGGCAGGTCAAAACAATGCTGCGTAAACAGAagGTGTCCAAATTTAGCAGTTCAAGAAGCCGAAGAGGATGCATTGGCTTCTCAAGATGAAGAAGAACCAGAACTGAAATCACCAAGTAAAACAGATGTATCTCCCCCAAGACATCATCGAAAAGGTCAAGAGAAAAAAAGTTCTGTGAAGTGGGGATGTGAGTCAcatattgaaaagaaaaaaaaaaagctgtataAAGCAGTGTGTATTAACAATGAATTTATTAGTGTTGGAGACTTTGTACAAGTTTATCCGACAGATCCATCTGATCCATTGTATATCTGTCGTGTCATGTACATGTGGGAAGACTTAAATGGAGATAAGAAGTTTCATGCTCAGTGGTTATACCGCTCATCAGAAACAGTCCTTGGAGAAGTTGGTGACCCatgtgaagtttttttatctgatgATTGTGATGATATTAAACTTGGAGCAATTATGTCTAAGTGCaagGTTAATTATAAATCAGTGAGTGAAAACTGGTTCATGGAAGGAGGAAAGGAAGACTATATAACTTCAGATGATCGCCATGAACTCTTCTACCAGAAGTGGTATGATTATGAAGATGGTCTTTTCACTGATCCCCCTGATGAGTttcttatttcaaagtttgaagACAAGTTTTGTCCAAGCTGTGATCACGtcaaaacaaagcaaaagCTCAGACAGCTTATTTTAGGAGATGAAGTTGAAGTGGAAGACTCAATAAAATCTGAATCTTATttcaaaacAATCTCTTGGGAAGGTATTTGTTATGGCATAGGTGATTGTGTTTACTTAGATCCTGAAGCTTTTACATTCAAGATTAAACAGAAACCAGAGgtgcaaaaaagtaaaattttatccaaggatGAGGATGAATATCCGGAACTTTATCGGAAATCAAATGATTATATCAAAGGGagcaatataaatatttcagagCCCTTTAGGATAGgaaaaataattagcattataaaaaaaaaagacagttATGGGGGAGAGAAATCTATAATGTTAAAAGTTAGAAAGTTTTACAGACCAGAAAATACTCACAAGGGAAAGTCACTGACAATGAATTGTGATCTAAACATGGTTTACTGGAGTAATGAAgAAGCCACTGTCGATTTTAATAATGTAGAAGGTAAATGTTATGTTCTTTATGCTGATGATGCTGATATGGATATGGTTAAGTTTACTGAGGCAGGACCACATCGGTTTTATTTCAGAGAagcatatgatgcagaaaagaaagaatttgATATTCCCCCCAGAGAAGCATGGAACTCCAATAAGggGAAAGGGAAAGCAAAAGCATCAAAGCAGGAGTCTGGGATTGAAGTAGATTTTCCCATTTATGAAAAAgtcgaaaaattaaaagcattagATATATTTGCTGGTTGTGGtgGTTTATCCGAGGGTCTTAATCAAGTGGGAGTGGTAAATAGCTTTTGGGCTATTGAGTTTGAACCTTCAGCTGCGCAAGCTTACAGATTAAATAATCCTAATACTATTGTATTTAATCTTGACTGTAACAGTGTGCTAAAGCAGATCATAGAGGGCAAGGAGAAAGACGAATTAGGACAACGCCTGCCCCGTCGAGGTGAAGTAGATATATTGTGTGGCGGACCACCTTGTCAAGGTTTTAGTGGAATGAATAGATTCAATCAGAGAGAATATTCCATGTTTAAgaaTTCGTTGGTGACATCATATCTTAGCTATTGCGATTATTTTCGTCcgaagtttttcattttggaAAATGTCAGAAACTTtgtttcgtttaaaaaaagtatggtaTTGAAGCTTACTTTAAGTTGTTTGGTCAAAATGGGGTATCAGTGTGAGTTTGGGGTACTACAAGCTGGTTCTTACGGCGTTCCTCAAACCAGACGACgTGCCATCATAATGGCTGCTGCCCCTGGGGAAATTCTCCCTAAATTCCCTGAACCTCAACACGTATTTGCATCGAAAGCACTCTCTTTGTCTGTTACTATAAATGGTCATAAGtatcaAGCCCTGAAGCGGCTGCATTCTGCAGCCTATCGGACTACTACAGTATACGATGCGATGAGTGATCTTCCGGAAATCAAAAACGGTGCAAATAAGTTAGAAATTGCCTACGATAGTGAAGCGTTGacacattttcaaaaaaagatacGTGATAAACACGTACAAATTCTTCGTGATCATATATGTAAAGATATGAGCCCTTTAGTAGAAGCCCGCATGAGTTATATACCATGTCAACCAGGATGTGATTGGAGAGATCTTCCTAACAAAGCTGTTAAACTAAGAGACGGAAGCATGACGAAGATACTCCTATATCTTCATAATGACAAGAAACAAGGTCCTAGTAAAAACGGAGGAAAACGCGGTGTATGTGCATGTGCTAACGGTAAAGCATGCGATCCATCGGACCGTCAGTTTAACACATTGATTCCGTGGTGTTTACCTCATACTGGTAATAGACACAATAATTGGGCTGGCCTCTATGGAAGATTAGAATGGGATGGATTTTTTAGTACAACTGTTACCAATCCAGAGCCTATGGGAAAACAAGGTCGTGTGCTACATCCAGAGCAACATAGAGTTGTCAGTGTGCGCGAATGCTCCCGTTCACAAGGCTTTCCTGATTCATTTCGTTTTTATGGCAATATACTAGATAAGCATAGACAGattgGCAATGCAGTAGCGCCTCCTATGTCTGCTGCCATCGGacaagaaataagaaaaagtattgTCGCAAAAAAGTTACGACGTGAACTTGGAAATCATGAAAAATTGAAGCAAGAAAGCTAG

Transcript

BRAKERKRET00000026481

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q27746	DNA (cytosine-5)-methyltransferase PliMCI OS=Paracentrotus lividus OX=7656 GN=DNMT PE=2 SV=1
Q92072	DNA (cytosine-5)-methyltransferase 1 OS=Gallus gallus OX=9031 GN=DNMT1 PE=1 SV=1
P26358	DNA (cytosine-5)-methyltransferase 1 OS=Homo sapiens OX=9606 GN=DNMT1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003199 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00145 all species →	DNA_methylase	C-5 cytosine-specific DNA methylase	Domain	Interproscan
PF02008 all species →	zf-CXXC	CXXC zinc finger domain	Domain	Interproscan
PF12047 all species →	DNMT1-RFD	Cytosine specific DNA methyltransferase replication foci domain	Domain	Interproscan
PF01426 all species →	BAH	BAH domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002857 all species →	Domain	Zinc finger, CXXC-type	Interproscan
IPR043151 all species →	Homologous_superfamily	Bromo adjacent homology (BAH) domain superfamily	Interproscan
IPR018117 all species →	Active_site	DNA methylase, C-5 cytosine-specific, active site	Interproscan
IPR001525 all species →	Family	C-5 cytosine methyltransferase	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR001025 all species →	Domain	Bromo adjacent homology (BAH) domain	Interproscan
IPR050390 all species →	Family	DNA Cytosine-5 Methyltransferase	Interproscan
IPR017198 all species →	Family	DNA (cytosine-5)-methyltransferase 1-like	Interproscan
IPR031303 all species →	Conserved_site	DNA methylase, C-5 cytosine-specific, conserved site	Interproscan
IPR022702 all species →	Domain	DNA (cytosine-5)-methyltransferase 1, replication foci domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10629 all species →	CYTOSINE-SPECIFIC METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0003886 all species →	Molecular Function	DNA (cytosine-5-)-methyltransferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0010216 all species →	Biological Process	obsolete negative regulation of gene expression via chromosomal DNA cytosine methylation	Interproscan
GO:0010424 all species →	Biological Process	obsolete DNA methylation on cytosine within a CG sequence	Interproscan
GO:0006346 all species →	Biological Process	DNA methylation-dependent constitutive heterochromatin formation	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
K00558	DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1	EC:2.1.1.37	Prokaryotic defense system	ko02048	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000026481.1 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.