Gene detail

Detailed information of BRAKERKREP00000011534.1 in Hydra viridissima

Genomic Location: QPEY01000055.1:141738...147105
NR annotation: XP_047140638.1, nonsense-mediated mRNA decay factor SMG5 [Hydra vulgaris]
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
F1R7R1	Nonsense-mediated mRNA decay factor SMG5 OS=Danio rerio OX=7955 GN=smg5 PE=2 SV=1
Q6ZPY2	Nonsense-mediated mRNA decay factor SMG5 OS=Mus musculus OX=10090 GN=Smg5 PE=1 SV=2
Q9UPR3	Nonsense-mediated mRNA decay factor SMG5 OS=Homo sapiens OX=9606 GN=SMG5 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006041 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10373 all species →	EST1_DNA_bind	Est1 DNA/RNA binding domain	Repeat	Interproscan
PF10374 all species →	EST1	Telomerase activating protein Est1	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018834 all species →	Domain	DNA/RNA-binding domain, Est1-type	Interproscan
IPR019458 all species →	Domain	Telomerase activating protein Est1-like, N-terminal	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR045153 all species →	Family	Est1/Ebs1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15696 all species →	SMG-7 SUPPRESSOR WITH MORPHOLOGICAL EFFECT ON GENITALIA PROTEIN 7	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0005697 all species →	Cellular Component	telomerase holoenzyme complex	Interproscan
GO:0042162 all species →	Molecular Function	telomeric DNA binding	Interproscan
GO:0070034 all species →	Molecular Function	telomerase RNA binding	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 BRAKERKREP00000011534.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000011534.1 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

10.3Max TPM

2.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	2	0.98	10.26
Whole	6	5	5.90	8.59
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	4.09	4.09
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	4.11	4.11
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	TPM
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	10.26
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	7.46
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
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	8.59
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	8.42
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	7.06
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	5.68
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	5.66
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	4.09
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	4.11
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.00
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.