Gene detail

Detailed information of BRAKERKREP00000010046.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_012565729.1, homeobox protein vab-15 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q09604	Homeobox protein vab-15 OS=Caenorhabditis elegans OX=6239 GN=vab-15 PE=2 SV=1
Q623D4	Homeobox protein vab-15 OS=Caenorhabditis briggsae OX=6238 GN=vab-15 PE=3 SV=1
P52953	Homeobox protein MSX-2 (Fragment) OS=Rattus norvegicus OX=10116 GN=Msx2 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008985 (this species only)
Transcription factor family	Homeobox · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020479 all species →	Domain	Homeobox domain, metazoa	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR050674 all species →	Family	Msh Homeobox Transcriptional Regulators	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24338 all species →	HOMEOBOX PROTEIN MSX	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0048598 all species →	Biological Process	embryonic morphogenesis	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
K09341	MSX; homeobox protein MSX	-	Transcription factors	ko03000	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000010046.1 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

12TPM > 0

7Conditions

5.4Max TPM

1.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	3	0.34	4.29
Whole	6	5	3.60	5.41
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	3.79	3.79
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.56	0.56
symbioic hydra M9 strain · symbioic hydra rep1	1	1	3.19	3.19
symbioic hydra M9 strain · symbioic hydra rep2	1	1	2.94	2.94
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
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	4.29
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	0.92
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.88
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
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	5.41
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	4.76
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	4.21
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	4.05
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	3.15
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	3.79
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.56
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	3.19
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	2.94
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.