Gene detail

Detailed information of BRAKERKREP00000023587.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:719543...721462
NR annotation: WP_053246050.1, tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG [Achromobacter sp. DMS1]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A9IJ48	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG OS=Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448) OX=340100 GN=mnmG PE=3 SV=1
Q7WRF1	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=mnmG PE=3 SV=1
Q7W0T0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) OX=257313 GN=mnmG PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0014477 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01134 all species →	GIDA	Glucose inhibited division protein A	Family	Interproscan
PF13932 all species →	GIDA_C	tRNA modifying enzyme MnmG/GidA C-terminal helical bundle	Domain	Interproscan
PF21680 all species →	GIDA_C_1st	tRNA modifying enzyme MnmG/GidA C-terminal helical domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004416 all species →	Family	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG	Interproscan
IPR044920 all species →	Homologous_superfamily	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain superfamily	Interproscan
IPR020595 all species →	Conserved_site	MnmG-related, conserved site	Interproscan
IPR040131 all species →	Domain	MnmG, N-terminal domain	Interproscan
IPR026904 all species →	Domain	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal	Interproscan
IPR002218 all species →	Family	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related	Interproscan
IPR047001 all species →	Domain	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain	Interproscan
IPR036188 all species →	Homologous_superfamily	FAD/NAD(P)-binding domain superfamily	Interproscan
IPR049312 all species →	Domain	tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal, N-terninal subdomain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11806 all species →	GLUCOSE INHIBITED DIVISION PROTEIN A	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0002098 all species →	Biological Process	tRNA wobble uridine modification	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0008033 all species →	Biological Process	tRNA processing	Interproscan
GO:0030488 all species →	Biological Process	tRNA methylation	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide 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
K03495	gidA, mnmG, MTO1; tRNA uridine 5-carboxymethylaminomethyl modification enzyme	-	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 BRAKERKREP00000023587.1 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.