Gene detail

Detailed information of BRAKERKREP00000022761.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:685913...686224
NR annotation: WP_066124752.1, 50S ribosomal protein L6 [Bordetella ansorpii]
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
Q2L270	Large ribosomal subunit protein uL6 OS=Bordetella avium (strain 197N) OX=360910 GN=rplF PE=3 SV=1
A9IHT3	Large ribosomal subunit protein uL6 OS=Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448) OX=340100 GN=rplF PE=3 SV=1
Q7WRA8	Large ribosomal subunit protein uL6 OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=rplF PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0022485 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00347 all species →	Ribosomal_L6	Ribosomal protein L6	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036789 all species →	Homologous_superfamily	Large ribosomal subunit protein uL6-like, alpha-beta domain superfamily	Interproscan
IPR020040 all species →	Domain	Large ribosomal subunit protein uL6, alpha-beta domain	Interproscan
IPR000702 all species →	Family	Large ribosomal subunit protein uL6-like	Interproscan
IPR019906 all species →	Family	Large ribosomal subunit protein uL6, bacterial-type	Interproscan
IPR002358 all species →	Conserved_site	Large ribosomal subunit protein uL6, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11655 all species →	60S/50S RIBOSOMAL PROTEIN L6/L9	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	Interproscan
GO:0019843 all species →	Molecular Function	rRNA binding	Interproscan
GO:0002181 all species →	Biological Process	cytoplasmic translation	Interproscan
GO:0022625 all species →	Cellular Component	cytosolic large ribosomal subunit	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
K02933	RP-L6, MRPL6, rplF; large subunit ribosomal protein L6	-	Ribosome	ko03011	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022761.1 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

17TPM > 0

7Conditions

41.3Max TPM

9.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	7	5.81	41.31
Whole	6	6	10.34	12.38
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	29.00	29.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	29.84	29.84
symbioic hydra M9 strain · symbioic hydra rep1	1	1	16.78	16.78
symbioic hydra M9 strain · symbioic hydra rep2	1	1	19.31	19.31
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	41.31
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	29.96
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	17.56
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	10.16
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	5.55
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.09
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.05
SRR21134051	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
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	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
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	12.38
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	12.24
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	12.19
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	12.03
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	11.92
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	1.31
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	29.00
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	29.84
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	16.78
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	19.31
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.