Gene detail

Detailed information of BRAKERKREP00000012465.1 in Hydra viridissima

Genomic Location: QPEY01000063.1:462783...475330
NR annotation: XP_047140408.1, interferon regulatory factor 5 isoform X3 [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
Q3SZP0	Interferon regulatory factor 1 OS=Bos taurus OX=9913 GN=IRF1 PE=2 SV=1
A0FIN4	Interferon regulatory factor 1 OS=Sus scrofa OX=9823 GN=IRF1 PE=2 SV=1
P10914	Interferon regulatory factor 1 OS=Homo sapiens OX=9606 GN=IRF1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000568 (this species only) · gene tree & orthology
Transcription factor family	IRF · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00605 all species →	IRF	Interferon regulatory factor transcription factor	Domain	Interproscan
PF10401 all species →	IRF-3	Interferon-regulatory factor 3	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001346 all species →	Domain	Interferon regulatory factor, DNA-binding domain	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR019471 all species →	Domain	Interferon regulatory factor-3	Interproscan
IPR017855 all species →	Homologous_superfamily	SMAD-like domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11949 all species →	INTERFERON REGULATORY FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000976 all species →	Molecular Function	transcription cis-regulatory region binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0002376 all species →	Biological Process	immune system process	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	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
K01154	hsdS; type I restriction enzyme, S subunit	EC:3.1.21.3	Prokaryotic defense system	ko02048	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000012465.1 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

30.7Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	8	2.73	30.70
Whole	6	6	2.20	12.69
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	0.01	0.01
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.01	0.01
symbioic hydra M9 strain · symbioic hydra rep1	1	1	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
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	30.70
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	8.57
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	4.41
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	3.69
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	1.15
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.37
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.17
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	0.08
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	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
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
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	12.69
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.41
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.06
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	0.03
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	0.01
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	0.01
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	0.01
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.01
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.