Gene detail

Detailed information of BRAKERKREP00000013799.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_012562913.1, glycine betaine transporter 1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000013799

ATGGATCAGATACATAAAGCTTTTCTAGACGACGAGActcaaaaaaaggtttgtcaTATAACCAACACATGCGCAAAGacgattttcaaaaaagataacGAAAAAACTAACGACAGGTGTCTAAATGTGAAAGGGAAGTTTGGACCTTTTCAGTTTTACTTTAATCCGTTGACAACCAGTTTATCTGCAATTATTATTTGGGCTTTTGTTGTTTGGTGCATATTTAGACCTATAGAGTCTTATAGCGAGATATCAAAATGGAAGATATGGATTACTCAAAAATGGACATGGCTTTATATTGGGACACGAGATATTTGGGCTTTATTCATCGtagtaatttacttttcgAAGTATTCTTCGCTGAAAttagGTCGCGACGATGAAAAACCAGAATTTTCTGATGGAGCATATTTCACAATGCTATTTTCTGCTGGCATTGGTGTTGGTCTCTTTTATTTTGGAGTTGCTGAACCTGTCTATCATTATGCACCAGGTCGCGATCGAAATAGATACTGGGGCAgGTACAACGATAACCAGCGAGCGCAAGATGCAATGAACTTGTCTTTTTTTCATTGGGGTATTCATGGATGGATTGTTTATGTACTCATTGGTTTGCTACTTGGAGTTCTTTCCCATAGACGAGACTTGCCAATGACGATGCGAACTTGTTTTTATCCGCTATTAGGAGATAAAGTGTTTGGCTTTTTTGGAGATTTTATTGATACATTATCTATTATTTGCACAATGCTCGGGGTCTGTACTAGTCTAggCTTAGGCGTCATTCAATTAAACAGTGGTCTAAGCCGATTGCATAAAGGTATTGACGAGTCTTCATCTAACCAGATCATCATTATATGGTGTGTAACTTTAATAGCAACAGCTTCAGTTGTGAGCGGCGTTAAGATAGGAATCAAATGGCTATCTGAAATATGTTTTATGGTTGgaACAGTTATACTACTCGTAGTCTTCTTTTCTGACGACACTTGGTTTTTACTAAATCTCTTCGTTCAATCCTGTGGTTATTACGCACAAAATTTTGTAGAGGTTGGATTTCATACAGATGCATTTGCAATGAAAGGTGATGCTCCCGACGGGAAGCAAGCTCCAGGCTGGATGGATGCATGGACTCTTTTCTACTGGGGATGGTGGGTTAGCTGGTCCCCGTTTGTGGGGATGTTTTTTGCCAAAATTAGCCGAGGACGAACTATTAAAGAGTTCATAACATACACACTCACTGTAccaatattttatacttttttttggttaactGTATTTGGAGGAGCAGGCTTAGCCATGGAGCGAAAAGCCGAAGGTCTTAACATCACCTGTGAAATGTACAACACAACTTTGTTTCCGACATATGGCTCTCAAAAAATTAAGCAGTTGTTTGGGGCTCACCGATTATCTTGTCGTCTTTCAACAGACATGTGGTTTGATGTTATTGAACAATATGGTGAAATTGGTTCAGCTCTTTCTGTTTTTTCCATCGTTGGTCTTGTTTTATACTTTGTCACATCTTCCGATAGTGGGTCTTTAGTTATTGATTGTCTTTCAGCGAACGGTAATCCAGATCCACCTATCCTCCAGAGAATATTTTGGTCTTTCACCGAAGGTGCAACTGCAACAGCCCTACTAAAAGCCGGCGGTAAAAATGCACTTGTAGCCCTACAAACAGCGTCCGTTTGTGCAGGGTTGCCTTACAcgtttatcttaaattttgcTTGCGTATCTTTGTGGcgaattttgaaaatagaagCAGGGGATTTAGACGAAGACGAAGGAAAATGGAAAGTCGGGTTGTTTGAttgtttaacaacaaaatcacaattgaaaaaaagtcttttcgCTGTGATAGCACCATGGTATCTGCTTGCAGACACGGCCGCAAATGTTGAGGCgaaaaaaagagtttactTTATTGCACATAGCATAATTTATGCTGTTCTATTTTACGGTTGGATTATATTGATGGTTTgcgaaaaaaaagttgaggGGATTTCTTTTGTGGGTTGGGTCGCtcttgttactttttttggaTACGCTTGTCGCGTGCGAGGTACTGTTCGTGAAAAATACAAGCTACAGGGAAATATAGTGGAAGATTTCTTTAGTCTCTGTTTGTTATATCCATGTGCTGTATTTCAACTGCACGAGCAAGTCAAGTATGaggagaaaaaaatcttagggAGCATCTCGAAGCAAAATAGCAGCGGAGAAGAATGCGATAACaataaagatgttaaaattgatttgtag

Transcript

BRAKERKRET00000013799

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A0A0B5RUB0	Trimethylamine transporter OS=Myroides profundi OX=480520 GN=tmaT PE=1 SV=1
Q87PP5	Glycine betaine/proline/choline/ectoine transporter VP1456 OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) OX=223926 GN=VP1456 PE=1 SV=1
Q6F754	Glycine betaine transporter OS=Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) OX=62977 GN=ACIAD3460 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000591 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02028 all species →	BCCT	BCCT, betaine/carnitine/choline family transporter	Family	Interproscan
PF04749 all species →	PLAC8	PLAC8 family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018093 all species →	Conserved_site	BCCT transporter, conserved site	Interproscan
IPR000060 all species →	Family	BCCT transporter family	Interproscan
IPR006461 all species →	Family	PLAC8 motif-containing protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30047 all species →	HIGH-AFFINITY CHOLINE TRANSPORT PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0071705 all species →	Biological Process	nitrogen compound transport	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006810 all species →	Biological Process	transport	Interproscan
GO:0016021 all species →	Cellular Component	membrane	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

No KEGG orthology assignment for BRAKERKREP00000013799.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000013799.1 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

16TPM > 0

7Conditions

6.1Max TPM

1.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	7	1.12	6.07
Whole	6	5	2.31	3.01
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	1.82	1.82
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	1.42	1.42
symbioic hydra M9 strain · symbioic hydra rep1	1	1	1.36	1.36
symbioic hydra M9 strain · symbioic hydra rep2	1	1	0.09	0.09
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
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	6.07
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	3.63
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	3.45
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	3.12
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	2.06
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	1.71
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	0.10
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
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
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	3.01
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	2.89
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	2.75
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	2.62
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	2.62
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	1.82
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	1.42
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	1.36
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	0.09
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.