Gene detail

Detailed information of BRAKERKREP00000022673.1 in Hydra viridissima

Genomic Location: QPEY01000524.1:681168...681599
NR annotation: NLY27979.1, 30S ribosomal protein S4 [Alcaligenaceae bacterium]
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
P0A4C6	Small ribosomal subunit protein uS4 OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=rpsD PE=3 SV=1
P0A4C7	Small ribosomal subunit protein uS4 OS=Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) OX=257311 GN=rpsD PE=3 SV=1
P0A4C5	Small ribosomal subunit protein uS4 OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) OX=257313 GN=rpsD PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0016704 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00163 all species →	Ribosomal_S4	Ribosomal protein S4/S9 N-terminal domain	Family	Interproscan
PF01479 all species →	S4	S4 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001912 all species →	Domain	Small ribosomal subunit protein uS4, N-terminal	Interproscan
IPR022801 all species →	Family	Small ribosomal subunit protein uS4	Interproscan
IPR036986 all species →	Homologous_superfamily	RNA-binding S4 domain superfamily	Interproscan
IPR002942 all species →	Domain	RNA-binding S4 domain	Interproscan
IPR018079 all species →	Conserved_site	Small ribosomal subunit protein uS4, conserved site	Interproscan
IPR005709 all species →	Family	Small ribosomal subunit protein uS4, bacterial-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11831 all species →	30S 40S RIBOSOMAL PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0019843 all species →	Molecular Function	rRNA binding	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0015935 all species →	Cellular Component	small ribosomal subunit	Interproscan
GO:0042274 all species →	Biological Process	ribosomal small subunit biogenesis	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006412 all species →	Biological Process	translation	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 BRAKERKREP00000022673.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022673.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.