Gene detail

Detailed information of BRAKERKREP00000001802.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047136943.1, sorting nexin-13 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001802

atgGTAGAGACAATAAATAGTTCTACAAAGAATGTACAGattGTTTTGCCTTCAAACCTGTTGTGGattttattagcatttttcttgtattttgtTACATTTGGAGTGATTGGTGCTCTGTTTTCAGTTGTATATGTTCTGCTCTTTATTGCTGGATTCATTGTAGTCATTGGCAAATGGAACATTAAGAGATCACAGGATATCCTATTATCAGATGATATAGAGTTACTAGCatttgaagataaattttgCGGTATACCTGccatcttcaaaaaaatcaatgaagcTCCACATGGCTACAAATATGATAAACGGATGACAGGTTCTAGCTGTATAGATGATGTCATTCAAGAGAtactgcaattttttttacgggATTACATACATAATTGGTATTTATCAATAACAGATgatgaaagatttttgtatGAATTGCGCCAAACTATTCAGcacataattattttgttttcatcaagGTCAAAAGAGGTGCAATGGGTGCCATTTCTGACTACCCGCTTGGTTGATATTTTTGCCACACATTTGCGTATTTTTCGAATAACTAAAGAACGGCttgagagaaaaaataatgtgAGTAGTTTATCAAAAGAAGAAACACAAGCTCAAGCTGAAATTGATCttgaagaaatgttttttgctgTTGAAGCGGAAGTTGAAGGAGTCAGTAGGCAGCCAGTATGTCTTGATGATGAAGTTGAGCAGAAGTATTTGCAAGATGTTACTGAATTGCTACTTTATCTGCTTCTGCCACCAGAGCAGTTTCGAGACAAACTTGTGCGATCTTTTCTGCTTGAAATTATAGCTACAAGTGTATTTTTGCCTACCATTAAAATGGTGTGTGATCCAGATTATGTAAACCAAAATATATCATGGATGtgcaATAAAGATACTACTTTTACTGTTGAGGCTTTTTTGACAACAATTAGATACAGTACTGATGTTGATGATATAGAAGagacaaaaaagaaagtagaTTTAGAAATAGCGAAGCTTCGTTCTCAAGATTCACATGTTCTTGaatCAAACGATTCAGAGATGAGTGTAAAACAGCAGCTCAATAGTTTGATGTATGTTCGCAAACTCTGTGTGACTACAATAAAGCGTTTAAAGAATGGTCGAGCAGAAGAAGCTTCACTTACTTTAGAAGATCCCGAGCAAGACCTTATGGAAATGTTCCCTCCGACTCAAAATCTGCCCAAGTTATcgcttaaagaaatttttgaagataatacagcattatcttattttattgaattcaTGGGTACATACAACGCAGAACATTATGTATTCTTCCATTTAACTATTGAGGGCTTCCGTGCAACAGCCATTCAACAGCTGTGCATTCTTGCTGAGGAGACAACAAAAGCccacaataaaaaacttgctgtgCCTTCATCTGAGAATTTTGAACAGCTTCGGCAAGCCGCTCTTAATATTTACGAGGAATACCTTTCTCAGAGGGCGAGTCCTCGAATTGTACTCGATGATCAACTAGTccgaaagatttttaaagatattaaaagtAACGAACCAAGTGGAGCCTATTTTGACAACGCACATATGGCTGTTTACAAGATTCTAGCCAGTCAAAAGTATTATGGAACGTTTTTAAACAGCACAGCTTATGTGAAGTGTTTGTATGAGTTGGATTTGCTAAACAAATCTgaagatgaTCAGTCTTTTCATCCGACAGatGATCGACCCAGGTCAATGTCTTCTATGTCTACTCGTTCAAAGTTATCTCACGAAGAGTCCTCTCTGGTGCAACCATGGACGCCAGACAATGACTTGAGATTTTCTGCTCTTATAGGTCAAGctaacataataaataatggCAGCAAATCCTACGCAATATACACCATTCATGTTTGTCGGACTACAAGCGAAGGGTCTAGAAACTGGACTGTGATACGGCGTTACTCGGATTTTCACGATTTTCATATGCAGATTAGAGAAAAGtACGAATCACTGCATTGGCTGCACTTACCTGAGAAAAAAACGTTCGGTAATATGGACCAAGATTTCattgataaaagaaagaatgcccttgaaaattatttacagCCATTACTTGAAACAACTCTGCTGTCAGAGAACCCCGGTTTGTTTGAGTTGGTTGCCGGTTTTCTTGAACAAGGAGAATACTACCCAGGAAAGTCAGCAATGGCCAGAAagattgatcACATTGTTAATCCCATTCAGAGTTCACTCTCCAACGTTTCTAGAGTTGTCAAATTGAAAACTGACTTTcgtaccattaaaaaaaataactcagCGGCGGTGTGCATCTTATTagtgttTGACATGTTTCAACATTCCAATCTAAATAAACGATTGTTTTACGTCTGCTTCGAAGCTTTGATCGAAGAGATGTTTCctgataataaatttagagaaattttcaaaaaaattcatcaaaaaaagaagcctGCTTCgtga

Transcript

BRAKERKRET00000001802

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6PHS6	Sorting nexin-13 OS=Mus musculus OX=10090 GN=Snx13 PE=2 SV=1
Q9Y5W8	Sorting nexin-13 OS=Homo sapiens OX=9606 GN=SNX13 PE=1 SV=4
Q9Y2I1	Nischarin OS=Homo sapiens OX=9606 GN=NISCH PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003876 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00615 all species →	RGS	Regulator of G protein signaling domain	Domain	Interproscan
PF00787 all species →	PX	PX domain	Domain	Interproscan
PF02194 all species →	PXA	PXA domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR016137 all species →	Domain	RGS domain	Interproscan
IPR003114 all species →	Domain	Phox-associated domain	Interproscan
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR044926 all species →	Homologous_superfamily	RGS, subdomain 2	Interproscan
IPR036305 all species →	Homologous_superfamily	RGS domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22775 all species →	SORTING NEXIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0005769 all species →	Cellular Component	early endosome	Interproscan
GO:0043231 all species →	Cellular Component	intracellular membrane-bounded organelle	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
K17925	SNX13; sorting nexin-13	-	Domain-containing proteins not elsewhere classified	ko04990	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001802.1 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

14TPM > 0

7Conditions

10.1Max TPM

3.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	6	2.55	10.06
Whole	6	5	6.58	9.33
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	4.43	4.43
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	3.83	3.83
symbioic hydra M9 strain · symbioic hydra rep1	1	1	2.81	2.81
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
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	10.06
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	9.11
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	7.52
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	7.23
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	6.74
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	5.21
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
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
SRR21134064	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
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	9.33
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	8.25
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	8.21
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	7.09
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	6.57
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	4.43
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	3.83
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	2.81
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.