Gene detail

Detailed information of BRAKERKREP00000020575.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047137118.1, integrin beta-2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000020575

ATGCTAGTAACATTGCTCGTTCTGTCTGCAGTTATTTCAAATGTAATTGCTCaagatgaaAAGAAGTGTACTAAATGGTCTACATGTAGTGATTGCTTGCAGTCCAGTGGGCAATGTTATTGGTGTGAAGACAAAgacTTTAGTTTTCCTCGATGCAacttaaaaccaattttagaAAGtgatcaaaaatgtaaatcaatTAGTATTGAAGATGGTAGCAAAgcTCAAGAGAAAAACCTTCCATTCAGTTCCACAATTCAAGTACAGCCACAGGaagtatcttttaaattacGTCCAGCTCAATcccaatcatttaaaataagtgtAAAACCTGCACGTGACTATCCAGTACAACTCTACTATTTGATGGATATGTCAAAGTCTATGGAGGATGATcaacaaaagctaaaaacacTTGGAACAAAAATAGcTCAAGAGATAAGTGGAATCACTAAAAACTATCAATTAGCATTTGGCTCATTTGTTGATAAAACTGTTTCACCTTTTTCACAAATAGACATTCTTGACCGACCATGCAATTTATCAATAGGTGGGTATTGTGCACCTACATTTGGTTATAAACATAACTTTGATTTTGACAGCAATGCAACAAAGTTTGaggAAGCAGTAGCTGCACAAGTTATCTCTGGCAACTTGGATACACCAGAAGGTGGTTTTGATGGTCTTATGCAAGTTTCTGTCTGTGATACgAAATTGGGCTggaaaaacaaagatttagCTCGTCGAATCGTAGTTTTTGTAACTGATGCTAGTCCTCATATTGCTGGAGATGGAAAAattggaGGTATCACAACACCAAATGATGGGCAATGTCATTTGAAAGACCAACAGGGTAGTACTATACTCAAGTTTTATGATATGTCTAATGAAATGgatTATCCATCCATCTCACAACTAAAGTTGAAActaaaagagaataaaattGTCCCAATCCTTGCTGTTACTGAAGATGTTTTTACTGTGTACCAAAAATTAGCTGAAGAATGGAAAGATACTGGAGCTGCTATTGGGAAGCTAAGTTCTGATTCATCTAATATTGTCGATTTAATCAGAGATAGTTATACGAAAATATCCACAACAGTTCGTTTGTCTGATGATTCATCAAAGAACATAGTAGTTCGATACAAAGGATCGTGCCAGTCATCAATAGAAAATGAGTGTCAGAATGTGAATATTGAAGAGCAAGTTGACTTCACTGTCACACTATCAGCATTGAGCTGCAACAGTGCAAAAAATGAGAATTTTACAGTTAACATTCCTGGTTTTGGTGAAGTCAAAGTAAATGTAGAGCTGATATGCGATTGTCCTTGTGAAAGATTAGCTGGAACTCCTAATTCTGATGACTGTTCTAAAAATGGCACATCTAAATGCGGTATATGTTATTGTAACCCAGGTCGTTATGGAACAAAGTGTGACTGTGATAACAAAGCCCAAGCTGATACATCTCTCTGTAAAATCACCAATTCTACAGATGAACAAGTCTGCAGTGGTTTTGGGCTTTGTGTGTGCGGTCAGTGCGAGTGTTTTAATCGCCCaAAAGCGAGCGATTCTACTGAAGTGGAGCGAATCTATGGAAAGTATTGTCAATGCAATAACTTTGGATGTGATAGATATCAAGGGAAAATATGCGGAGGACCTGATAGAGGAGTTTGTGATTGTCAAGAATGTAAGTGCAAGGAAGCTTTCCAAGGTAGTAACTGTGGTGCTGTAAATTGTACTATTGGTAGAAAGAACTGTATTAACAATGGacaaGTCTGCAGCAATAACGGTGAATGCGCTTGTGATACTTGTGTCTGTGAATTTGGTTACAAAGGAAAGTATTGTGAGAACTGCGTGTCTTGTCCTGGTAAATGTGCTAATGTCAAAGATTGCGTATTCTGTCAAGTCTATAACAAAGGAAAGCCTGAGGTGTGCTCGAAATGTGACCTTAACATTCGTATAGTTAACAAAACCGAAGAAAAATGCTCTTACCTCGACGACAATAATTGTTATGTCATTTTCAGCTTTGACAACGAGTTAGCCggtacaaaaaatgaaacaattttagttcaaaaagaaccaaagtgtaTTGTCATCATTACCACTGATCCTCCTATCCTGGCGATAGTACTCGGCACTATCGGAGGCATTGTTCTGCTCGGATTGATCTTGCTACTGTTGTGGAAACTTTTAATTACTGCTTATGATAACTATGAATACCATCAATTCGAGAAAGAACGAATGAAGTCCCAGTGGgaaaatGCTGAAAACCCAATTTACAAACCATCTAAACAACAGTTCCAAAACCCTACTTACGCTGGAAACAACTAG

Transcript

BRAKERKRET00000020575

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P12606	Integrin beta-1-A OS=Xenopus laevis OX=8355 GN=itgb1-a PE=2 SV=1
P12607	Integrin beta-1-B OS=Xenopus laevis OX=8355 GN=itgb1-b PE=2 SV=1
P07228	Integrin beta-1 OS=Gallus gallus OX=9031 GN=ITGB1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000809 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17205 all species →	PSI_integrin	Integrin plexin domain	Domain	Interproscan
PF18372 all species →	I-EGF_1	Integrin beta epidermal growth factor like domain 1	Domain	Interproscan
PF08725 all species →	Integrin_b_cyt	Integrin beta cytoplasmic domain	Domain	Interproscan
PF00362 all species →	Integrin_beta	Integrin beta chain VWA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036349 all species →	Homologous_superfamily	Integrin beta tail domain superfamily	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR014836 all species →	Domain	Integrin beta subunit, cytoplasmic domain	Interproscan
IPR015812 all species →	Family	Integrin beta subunit	Interproscan
IPR032695 all species →	Homologous_superfamily	Integrin domain superfamily	Interproscan
IPR033760 all species →	Domain	Integrin beta N-terminal	Interproscan
IPR002369 all species →	Domain	Integrin beta subunit, VWA domain	Interproscan
IPR012896 all species →	Domain	Integrin beta subunit, tail	Interproscan
IPR040622 all species →	Domain	Integrin beta, epidermal growth factor-like domain 1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10082 all species →	INTEGRIN BETA SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005178 all species →	Molecular Function	integrin binding	Interproscan
GO:0005925 all species →	Cellular Component	focal adhesion	Interproscan
GO:0007160 all species →	Biological Process	cell-matrix adhesion	Interproscan
GO:0007229 all species →	Biological Process	integrin-mediated signaling pathway	Interproscan
GO:0008305 all species →	Cellular Component	integrin complex	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0033627 all species →	Biological Process	cell adhesion mediated by integrin	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
K05719	ITGB1, CD29; integrin beta 1	-	CD molecules	ko04090	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000020575.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.