Gene detail

Detailed information of BRAKERKREP00000022801.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:9272...13964
NR annotation: KVN96777.1, hypothetical protein WJ69_02325 [Burkholderia ubonensis]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000022801

ATGGTTGGCAAAGACCCTTTAGTAGTACAAAAGGCCGAATACAACAAATCGGGCCGCAACGCCGCTGTGGTGaaattaaagttcaaaaatctACTTACCGCGTCGGCCAGCGAATCCGTATATAAGGCCGATGAAAAATTCGAGGTCGTACAGCTAGACCGTAAAGAATGTACCTACTCGTACTTTAGCGACCCCATGTACGTCTTTATGGATGCAGAATATAACCAGTATGAGATTGAAGCAGACAGCATGGGGGACGCCTTAAACTATCTAGAAGAAGGCATGCCTGTAGaagtagttttttatgaaggtCGCGCCATTTCGGTGGAGTTACCCACCACGCTTGTTCGCGAAATCACCTACACCGAGCCTGCCGTCCGTGGTGATACAGCAGCGCAAGGAAGAAGGGTGCCAAGGGTTTCAGGTTATCGAAGGGTCAACCTCAACCCCAGTGTGCAACATCACCGCCGACAAGTTGATGAATTCAATcgcaaatttattaaaaaccttgttcaaataaaaaatgccaGCGTTAGGCCGTCCGCAGAAACAAGCAGTCCGCCGCCCCTAGGGGGATCTCTCAATGAAGGCAATATTCGAGATTACGCTTCCTCCGACGCCACAAGAAATTTTCGACACGAATTCGTGTTTGCCGCCAAGGCGGAGAAGATTTCCTTTCCCTTGACGGCACTGCAATTCTTCGCGACGGTATATCCGGCACAGATTGGAACGAGACCCCCTGGCATACATCACAGCGAGCCCCAGGCATGGACGACGGGCGTCGCGAACAGGGCGCTGCCAGTCGCCAGCCCGCCGGATGCCCATCGTCCACCTATTCCCTCGATCCAATCGTTAACCCCGGGCACGGAATTCCCCCCCTCTAAGCAACGCCATCGCCGGCATGCGTCGACTGATACTCCCTCAGCCCCATGCATTGCAGCGCTGGCCACCGCAGGAGACAACGGCGCCCCGTATATAAGCGACCTACGCCGCAGACTAATCGACTGGGTCGACTGCGATAAAGTGCGAGCGCACGCGGACGACCCCTACGACTTGTTGCGGGCGGTGCTTGACCATTATGGGGAACCGCTACCCGATGACTTCAAGACGACATTGGACTTATCGCTTATCGAAGACGAGGGCCGCGTCGACGAGGCAGCGCTGCTTTATCACCAGCTGCAAAAAAGCCGAGAAACAACCACTGCCAGCAGCATTACTGCATTGTCGGAAGAACAGCTGCGTTCGCAATTTCTTGCGGCATTGCGTCCCGCCGTCGCGCGGCATAACGCGCTCGATAGGCTGTTTGCGCCGCCGGCGTTTAACGCAACAACAACGGCGCCCTTCTATGATGGCTTGGTCATGCGCAATGCCCTGGGTAAATCGTTCGAAGATTTGCTGAGCTCACCGGGCATCTCAGCCGACCCTGCTTTTGCTACCGCCAGCGTGTCATATAAGCGCGAATTGCTGACGGCGAAGTTCACGCAAATGGGGGAGAGCACGCAATACCCAATCGGCACGCCGCAGCATTCGCTCGCGAGCGTACTTAATCGCGTCGCAAAGTACGGTGAGCAAGCAGCACCTGCACCgtttgagaaagaaaaagacgTGTTAAACGCGTTTCAGGCCGTTACGAAAAAATGGAACGAAAACCGGTTGTCGTTCCCCATGAGCCCTGAACTGTTATTCGCCATGCATCTAGCGCAATCGAGCGGTGTAGCGCTACTGAGTACCGAGCAACTGTCGGCTCGGTACGATCACATTATGCAACAAGCCATCGACAGAGGTGATTGGGCTGTCCGAATCTGGTTACAAAGCATACCGAGGCGGTGGAATGCCGACGGCAAGCTGTGGACGAACCGAGAAAAAAACGTCAAGCGTGAAGCGCTGTTGGCAACATTCGACGCGCTGCGCCGGATGAGTTTTGGCAGCGAGAGGCCAGAGGGAGTAGCCGCGCCGAATGTATGGAACTTTGCAAAGCAAATTAAGGAGGCGGGACTGCTGGGGGAAATGTTGGTCGGAGACAATTGGGAAGAGAAGACGACTGCATTGTGGGACTATGCAAGTGAGCGCTTGTTTGCAGTGTACGGCAGGCCGCCTCTCTTTGTTCGAGCGAACGCCGCGCGCCAGATTCTCGAGAACTATGGCATGGGTGACGCCGAAATGGAGCGGGAACGCGACTACCTGCTTAATGCAGATAAGCCAAATCTTTCCCAACTAAAATTCGGCAGTCCTGTTGAAGAATTCCTTGATCGGGCCGAGTTGGCGAGGGTCAGCGACCACCAGATGAGAGTAGGCCGCCACCGGATCGATGCAAAAGAAGAACTGCAACGGTCAGAAGAGGAGTTTAACAACAACCTCCCGTCGAACGAATGGATTCGTGCGAAGGCAAAGGAAAACTTGCGTGAACAGGGTAGCTTGATCACTAACGCCACCCTAGATGCCGAAGTGGCGCAGATAGTGACTAAGTGTAGAGCACAGACGGAAGAGTACCTTGCATGGTGGCGTCGTTTTGAAGTATGGGTCAATATGCTACCTGTGATTGGACCCATCTATAACATCCAACAAGGCATACGTGAAAAGAATGTAAAACAAGTGCTATTAGGGATAGTCTTCCTGGGATTAGACATGCTAGATCTAGCCAGCGGCGAGCAGGGATCGCATGAGGGCGAGTTAAATATAAAGTCGATGTCAATGCATCACAGGTCAGCGATAGGCGACCTTCATCACGTAATGACGCAGCTGGGGGGCGGCACTATACCCGTGGCTCGTCACACCGAAGTTCATACAGCACCGCCGGCGTTCAGGCAACTGGATGGCAACGTGCCGCTTGAGCACCGCCCCCTAGCTAGGCGAGTACGCGCTAGAGAGACGGACGTGAAGTGGGGCGACTACGAAGTCGTGCTCATTGCCAACGAGAACCGAATTGTGCCAGTCCAGCACTCGGGTGGCTCATATTATGAAATCGACTGGTACACCGGTCAGCGGGCCAGGAATGCGCGGCTCATTAGTCGTGATACAGCCACGGGATTTCGCACCGACGGCGGCTTGCGGGGGGGAATGCGTAGTGACCGCTTAATCGATAGCGCAGGAAAGCCCATCAAAGATCTGCCTACCCCAACCGAAGTCCTAAGTAGCCTGCAGCCACCGACAACCAGCGTTGCGGTACCCGACCGGTTTGAGACCCTGTTTCACGCCTGCTTTGCGGTATATGAAACCAGACCCAACGCATTCCTCATGCCCAACACAGCTGGGGAGCTCTGGAGCGTGCAAAATTTTCTGAGCAACCTATATCAAAGAAGCTACACGTTCAAGCGCCTGCTAGACCACTACTTTTTGCGTCAACCGATAGGAGAAACGCTTTGGAAGATGTACTTCGGCGGTCTGCCGTCTGGACGGGGAGCCCGATCGGGCGAAAGAATCCCAGCGCGCACATACCCGGTGGGCAGGAAAATCGAATACCCAATATATAGCGATCTGGAGTACGGCGAATTTATGTCTGCTAGCGGAAAATCCCCTTTCACCAAAGAGACCGTCGTAGTTCATGAAGTAGTGCACGCTTTAACGGGTTTGCTAGATCCTCCTGACCGCCCCagagattttttgaatgcAAGAGTCCCACCACCCCCTCTTGACCGTGGAGGCGTTACTTATCTCTCCGACAAAATTCTCACCGAAGCAGGGTTTAAGGTTGAGGAGCGAGTGTGTTACTCCGACTTAACCGGGGGCGCACAAGATCCTCGACTAACAGACTTGATTGACAATGCTCATAAGGAAAATCTCTACCTCGACTCTCTCCTGGACGTACATCGATTTCCGGTGACAGCCGATACTATCGTCGAAGGCGTGCCGGTCAAGGACCGCATCACAGTCCAACAATGGCAGACGATTCAGAACCGGCTACACCAGCCCACGGAGGGCACGTCTGGCTCGGTGCGCCAACAATTCGCTGAGACATTCGACCTATCCCCCCCTGGCGTAAATGACAACCTTGCGGCGACGCAGATAAAGTCGGTCGCCGATGTGTGTAATCgatttatgcaaaaaagtgAGACGTTCCGAAAGCTCGTCAAGACGGCACCTGAAGCTGATAAGACGCGTCCATGGAAGTTCGAGTTTGATGCCGCCGCCGCTCCCAAAAATCCTGAGACGAGACGCGCACTTAGCGGCGTAGACGACGGTAGAAAACAAATCTACTTGTTTGAAGATGACACACAATATCTAACGGAGCGGGGCCTGCGCAACGTGGAGTTTGAACGCAAGGTCGCCAACGCCGTCATTCATGCTATGACAGATCTAAAGGTAGCAAAAACCGAGATTTACAGTAACCGCGGGGCGGCCACGCGTCTCGTCGACAAAGTATTAACAGAGTCGGGCTATCGTTATCCCAAACAAATCGTCGCCGGGTTAGCATCGTTGAACGATGCGTCGTCGGGCGTCAGACTGAAAGCCCGTCTAACTGCCGCGAGGCGCAGCATGGCCGTCGAAGAGGCCTATATGAATCAGGGTCATAGCGTTCCTCGTAGTTAG

Transcript

BRAKERKRET00000022801

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q2KXA0	Elongation factor P OS=Bordetella avium (strain 197N) OX=360910 GN=efp PE=3 SV=1
A9HX42	Elongation factor P OS=Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448) OX=340100 GN=efp PE=3 SV=1
Q7WLA9	Elongation factor P OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=efp PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0015554 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01132 all species →	EFP	Elongation factor P (EF-P) OB domain	Domain	Interproscan
PF08207 all species →	EFP_N	Elongation factor P (EF-P) KOW-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001059 all species →	Domain	Translation elongation factor P/YeiP, central	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR014722 all species →	Homologous_superfamily	Large ribosomal subunit protein uL2, domain 2	Interproscan
IPR020599 all species →	Family	Translation elongation factor P/YeiP	Interproscan
IPR008991 all species →	Homologous_superfamily	Translation protein SH3-like domain superfamily	Interproscan
IPR013185 all species →	Domain	Translation elongation factor, KOW-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30053 all species →	ELONGATION FACTOR P	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003746 all species →	Molecular Function	translation elongation factor activity	Interproscan
GO:0006414 all species →	Biological Process	translational elongation	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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 BRAKERKREP00000022801.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022801.1 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

9TPM > 0

7Conditions

15.1Max TPM

2.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	1	0.84	15.06
Whole	6	5	8.37	11.02
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	6.58	6.58
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	5.80	5.80
symbioic hydra M9 strain · symbioic hydra rep1	1	1	4.09	4.09
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
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	15.06
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
SRR21134064	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	11.02
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	10.40
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	10.25
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	9.73
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	8.80
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	6.58
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	5.80
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	4.09
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.