Gene detail

Detailed information of BRAKERKREP00000023631.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:1003762...1006509
NR annotation: MBB1595183.1, preprotein translocase subunit SecA [Achromobacter sp. UMC46]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000023631

ATGGTTTCTCTgctcaaaaaaatcataggCAGTCGCAATGACCGACTGCTTAAACAGTATCGCAAGCTAGTTAATCATATCAACGGCTTGGAGCCGCAGATGGCTGCGCTCTCCGATAGTCAGCTAGCGGCGAAGACGCAAGAATTTCGCACTCGCCACCAACAGGGCGCCTCGCTCAACGATTTATTGCCCGAAGCTTTTGCTGTCGTACGCGAGGCGGGCAAACGAGTGTTTGCCATGCGTCACTTTGATGTCCAGCTGCTGGGAGGGATTGCGCTGCACTATGGCAATATCGCCGAAATGCGCACCGGTGAAGGCAAGACGCTGATGGCCACGCTGCCGGTCTACCTTAACGCGCTCGCGGGCAAGGGTGTGCACGTGGTGACCGTCAACGACTATCTCGCCCGGCGCGATGCTGAATGGATGGGGCGCCTCTACCATTTTTTAGGGATGACGACCGCCGTCGTCGTGCCGCAGCAGCCTAATGACGAAAAGAAGGCAGCTTATACGGCCGATATCACCTACGGCACTAACAACGAGTTCGGCTTTGACTATCTACGCGACAATATGGAGTATCGCGTCGAGGATCGCCGCCAACGTCCTTTGTCGTACGCCATCGTCGACGAAGTAGATTCTATTCTGATCGACGAGGCGCGCACACCGCTGATTATCTCGGGTCAGGCGGAAGACCATACCGAGGTCTACGTTCGTATGAACGCGCTGCCGCCATTGCTACAACGTATGCAAGCTGAACCCAAACCGCATGAGCCTGAACCCGCGGGTGATTTTTGGGTGGACGAAAAAAGTCAGCAAGTCTATTTGTCTGAAGCGGGTCACGAGCACGCCGAGGCCACACTTGTGCGTCTAGGTCTGCTCCCCGAAGGGGAGTCAGTGTATGACCCGCGCCATATCGCGCTGATGCATCATTTGATGGTGGCGTTGCGGGCCCACACGTTGTTCTTCCGTGACCAGCAATACGTGGTGCAGGACGGCGAAGTCATTATTGTCGATGAATTTACCGGCCGTCTTATGGCTGGTCGCCGCTGGTCTGACGGACTGCATCAGGCAGTGGAAGCCAAGGAAGGGGTGACGATTCAGCTTGAGAATCAGACGCTGGCCTCTATCACCTTTCAAAACTACTTTCGTATGTATGAGAAGTTGGCTGGCATGACCGGCACCGCCGATACGGAAGCGTACGAGTTCCAGCAAATTTATGGGTTGGAGACGGTCATTATTCCCACCAACCGTCCCATGATACGCAAGGATCAGAATGACCAGGTCTTTAAGACCGCGCAAGAAAAGTACCACGCCATCCTAAACGACATTCGCGATTGCCACGAGCGCGGACAGCCCGTGCTCGTGGGTACCACGAGTATTGAGAATTCTGAATTGTTGTCGGGTCTGCTCAAGCAGGCTAAGTTGCCCCATGAAGTGCTCAATGCCAAGCAGCACGCGCGGGAAGCCGAAATTGTAGCCGAAGCTGGCAAGCCGGGTCGCATTACCATCGCCACCAATATGGCCGGTCGTGGTACGGATATCGTGCTGGGCGGTAGTGTCGACAAGCAGGTCGATCTTATACGCGCTGATATTTCGCTCGCggaagaagaaaaaacagtGCGTATTGAAAAAGTGCGCGCCGAATGGAAACCGCTCAATGAGCAGGTGAAAGCGGCGGGTGGCTTGCGAATTATAGGCACGGAACGACACGAGTCACGGCGCATCGATAATCAGTTGCGGGGCCGGGCCGGTCGTCAAGGCGATCCTGGCTCCTCGCGTTTTTACCTGTCCCTGGAAGATCCGCTCATGCGTATTTTTGCTGGCGACCGGGTACGCGCCATTATGGAGCGTCTTAAGCTTCCCGAGGGAGAGCCGATCGAAGCCGGTATCGTCACGCGTTCCATTGAAACGGCACAGCGCAAAGTGGAAGGCCGCAATTTTGATATCCGTAAGCAGCTTCTGGAGTACGACGACGTTGCTAATGACCAGCGTAAGGTTTTATACGCACAGCGCAACGAGGTGCTAGAGGCGGCTTCGGTTAGTGCCATGCTGGAAAATCTGCACGACGCGGTCATCACAGAGACGGTGCAAACTTACGTGCCGCTTGATTCGGTAGAAGAGCAATGGGACGTGTCGGCATTGCAGCGCGTGCTAGAAGCCGATTGGCGGATCGAGTTGCCGTTGGTCGACATGCTCAAGAACGAAAGCAATCTTACCGGTCAGGACATACTGGCTCGTGTACTGAAAGCCGCTCGCACCAATTATCAAGCCAAGGTCGAGCAGGTGGGGGCTGAAACTTGGGCGCACTTTGAGCGCTCCATTATGTTGCAGGCCATAGACCAGCATTGGCGCGAGCACCTGTCCGCATTGGATTACCTACGACAGGGCATCCACCTGCGAGGTTATGCGCAAAAAAATCCTAAGCAGGAATACAAGCGCGAAGCATTTGAGCTTTTTTCGGACATGTTAAGCCGCATCCGCAACGACGTGGTGCGTGTGCTTATAACGGTGCGTGTGCAGTCTGCCGAGCAAGTGGAGCAAGCTGAAGCGGCCCATCCTCATGTGCACAACGTACAGTTCCATCATTCTGATTACAGTGAGGCGCTTGCGGGTACGGGCTCAGATCGGCAGGTCTCGCCGCCGCGCCCAGCGCTCAAGCTCATGCCCCCTAGCCCTAAGGTCGGACGCAACGATCCATGTCCGTGTGGAAGCggcaaaaaatataaacattgcCACGGAAAGTTGCCCTAA

Transcript

BRAKERKRET00000023631

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A9I4Y3	Protein translocase subunit SecA OS=Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448) OX=340100 GN=secA PE=3 SV=1
Q7WFT1	Protein translocase subunit SecA OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=secA PE=3 SV=1
Q7VUR2	Protein translocase subunit SecA OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) OX=257313 GN=secA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0010693 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02810 all species →	SEC-C	SEC-C motif	Family	Interproscan
PF07517 all species →	SecA_DEAD	SecA DEAD-like domain	Domain	Interproscan
PF21090 all species →	P-loop_SecA	SecA P-loop domain	Domain	Interproscan
PF07516 all species →	SecA_SW	SecA Wing and Scaffold domain	Family	Interproscan
PF01043 all species →	SecA_PP_bind	SecA preprotein cross-linking domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036670 all species →	Homologous_superfamily	SecA, preprotein cross-linking domain superfamily	Interproscan
IPR044722 all species →	Domain	SecA, C-terminal helicase domain	Interproscan
IPR020937 all species →	Conserved_site	SecA conserved site	Interproscan
IPR000185 all species →	Family	Protein translocase subunit SecA	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR011130 all species →	Domain	SecA, preprotein cross-linking domain	Interproscan
IPR004027 all species →	Conserved_site	SEC-C motif	Interproscan
IPR011115 all species →	Domain	SecA DEAD-like, N-terminal	Interproscan
IPR036266 all species →	Homologous_superfamily	SecA, Wing/Scaffold superfamily	Interproscan
IPR014018 all species →	Domain	SecA motor DEAD	Interproscan
IPR011116 all species →	Domain	SecA Wing/Scaffold	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30612 all species →	SECA INNER MEMBRANE COMPONENT OF SEC PROTEIN SECRETION SYSTEM	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0017038 all species →	Biological Process	protein import	Interproscan
GO:0006605 all species →	Biological Process	protein targeting	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0031522 all species →	Cellular Component	cell envelope Sec protein transport complex	Interproscan
GO:0043952 all species →	Biological Process	protein transport by the Sec complex	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
K03070	secA; preprotein translocase subunit SecA	EC:7.4.2.8	Secretion system	ko02044	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023631.1 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

10TPM > 0

7Conditions

11.7Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	2	0.97	11.69
Whole	6	5	5.20	6.86
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	6.47	6.47
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	5.59	5.59
symbioic hydra M9 strain · symbioic hydra rep1	1	1	2.84	2.84
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	11.69
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	5.78
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
SRR21134057	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
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	6.86
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	6.50
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	6.30
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	6.09
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	5.45
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	6.47
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	5.59
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	2.84
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.