Gene detail

Detailed information of BRAKERKREP00000001200.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047126329.1, H/ACA ribonucleoprotein complex subunit 1 isoform X2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RJV1	H/ACA ribonucleoprotein complex subunit 1 OS=Xenopus tropicalis OX=8364 GN=gar1 PE=2 SV=1
Q6AYA1	H/ACA ribonucleoprotein complex subunit 1 OS=Rattus norvegicus OX=10116 GN=Gar1 PE=2 SV=1
Q9NY12	H/ACA ribonucleoprotein complex subunit 1 OS=Homo sapiens OX=9606 GN=GAR1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006523 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04410 all species →	Gar1	Gar1/Naf1 RNA binding region	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038664 all species →	Homologous_superfamily	H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain	Interproscan
IPR007504 all species →	Family	H/ACA ribonucleoprotein complex, subunit Gar1/Naf1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23237 all species →	NUCLEOLAR PROTEIN FAMILY A MEMBER 1 SNORNP PROTEIN GAR1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000454 all species →	Biological Process	snoRNA guided rRNA pseudouridine synthesis	Interproscan
GO:0031429 all species →	Cellular Component	box H/ACA snoRNP complex	Interproscan
GO:0034513 all species →	Molecular Function	box H/ACA snoRNA binding	Interproscan
GO:0001522 all species →	Biological Process	pseudouridine synthesis	Interproscan
GO:0042254 all species →	Biological Process	ribosome biogenesis	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 BRAKERKREP00000001200.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001200.1 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

26TPM > 0

7Conditions

1,909.9Max TPM

673.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	15	758.38	1,909.86
Whole	6	6	590.18	639.27
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	417.45	417.45
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	424.40	424.40
symbioic hydra M9 strain · symbioic hydra rep1	1	1	418.44	418.44
symbioic hydra M9 strain · symbioic hydra rep2	1	1	417.59	417.59
unannotated	1	1	671.24	671.24

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	1,909.86
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	1,532.80
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	1,322.70
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	1,278.80
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	1,273.92
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	1,227.35
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	1,158.35
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	615.33
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	584.59
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	532.88
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	506.43
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	457.32
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	449.84
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	418.59
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	382.08
SRR21134058	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
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	639.27
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	624.98
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	608.23
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	569.36
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	553.98
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	545.27
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	417.45
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	424.40
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	418.44
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	417.59
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	671.24

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.