Gene detail

Detailed information of BRAKERKREP00000019977.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047130170.1, nucleoporin SEH1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6TGU2	Nucleoporin SEH1 OS=Danio rerio OX=7955 GN=seh1l PE=2 SV=2
A7YY75	Nucleoporin SEH1 OS=Bos taurus OX=9913 GN=SEH1L PE=2 SV=1
C1BK83	Nucleoporin SEH1 OS=Osmerus mordax OX=8014 GN=seh1l PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005504 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR037363 all species →	Family	Sec13/Seh1 family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11024 all species →	NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0031080 all species →	Cellular Component	nuclear pore outer ring	Interproscan
GO:0034198 all species →	Biological Process	cellular response to amino acid starvation	Interproscan
GO:0035859 all species →	Cellular Component	Seh1-associated complex	Interproscan
GO:1904263 all species →	Biological Process	positive regulation of TORC1 signaling	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 BRAKERKREP00000019977.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000019977.1 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

20TPM > 0

7Conditions

63.3Max TPM

13.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	10	11.56	63.28
Whole	6	6	20.53	48.16
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	15.40	15.40
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	12.01	12.01
symbioic hydra M9 strain · symbioic hydra rep1	1	1	13.73	13.73
symbioic hydra M9 strain · symbioic hydra rep2	1	1	22.43	22.43
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
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	63.28
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	45.15
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	29.52
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	14.22
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	13.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	11.58
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	9.80
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	7.75
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	7.55
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	6.28
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	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
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	48.16
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	23.93
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	20.60
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	14.98
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	13.68
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	1.82
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	15.40
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	12.01
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	13.73
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	22.43
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.