Gene detail

Detailed information of BRAKERKREP00000022840.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:330713...331345
NR annotation: WP_033461691.1, MULTISPECIES: LPS export ABC transporter periplasmic protein LptC [Bordetella]
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)

No Swiss-Prot hit above the reporting threshold for this gene.

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06835 all species →	LptC	Lipopolysaccharide-assembly, LptC-related	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR026265 all species →	Family	Lipopolysaccharide export system protein LptC	Interproscan
IPR010664 all species →	Family	Lipopolysaccharide assembly, LptC-related	Interproscan

PANTHER

No PANTHER signature was recorded for BRAKERKREP00000022840.1 in Hydra viridissima.

Gene Ontology

GO term	Category	Description	Source
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015221 all species →	Molecular Function	lipopolysaccharide transmembrane transporter activity	Interproscan
GO:0015920 all species →	Biological Process	lipopolysaccharide transport	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
K11719	lptC; lipopolysaccharide export system protein LptC	-	Transporters	ko02000	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022840.1 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

1.3Max TPM

0.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	3	0.11	1.26
Whole	6	5	0.50	1.25
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	0.04	0.04
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.46	0.46
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.36	0.36
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
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	1.26
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	0.54
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.21
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
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
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	1.25
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.79
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.79
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	0.10
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	0.07
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	0.04
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.46
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.36
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.