Gene detail

Detailed information of BRAKERKREP00000001633.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047136937.1, vacuolar protein sorting-associated protein 16 homolog [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001633

atggacaTAGAACTATCAACCTTTTATGATGATACACCAGCTACCATTGATTGGAATCCATTAGGAGAGGTTTATTACAGaaaagttgaaatttatgATATGGCTTGGGTTAATCGCTTTGATCttagtaaatatataattgttgGATGTAATTTTGGAGGACCTATAGccATTACAAAAGAGGATAGTACAAGTGTAAGCAGTAATACAAAAAGTACCATCAATATATTCTCAGCATCTGGCATTGAGCAAGCTACtatcaaatgGGATGGtggaaaattaataaaaatggggTGGTCTAACAAGGAGGATTTACTATGCGTATCTGAAGATGGTGTTATGTACATTTATGACATGTTTGGTGAATATAAAAAGgaatcatctttttttgtgGAACCTCAAAGAGCTTTGATTTTGGAAGTAGAGATCTTTACCAGCAATTATGGAACTGGGATATGTTTGCTGACTAGTGAATACCAGTTCTTTGTGgcacaaaatatttatgatataaagCTAAACCGTTTGCAATCTCCATTTGCTCTTGAATCCCCTCCTAGCAGTTGggctgttttaaatttaccagATAAGCAATCTACAGTATTAATGGCCATTGATAGTGCTCTTTACGAGCTTGACACTTTTCAGCACAAATCAaagAATCCACTCATTAGCCACCCTGTGACttcattcattaaaatttctgtttcaTTTAACCAAAAGTATGTTGCTATGTTTGCTGATACAGGACTGCTCTGGATTGGGTCCTCTGACCTATcgGGTGTTTATTGTCAACATAACTCTCATTTACAAATATGCCCCTTGCAGCTTGTTTGGTGTGGGTCTGGGGCTGTGGTTGGACATTGGGATAACTATCTGTTAGTGGTAGGACCAAAACAAGAcactttaaaGTATTTTGTAGACACTAATGTACACTTGGTCCAGGAACTGGATGGAGTAAGGCTAGTGGGGAACAAGATTACAGAGTTTCTTCAAAAAGTACCTgAGGAAGTTGAAGATATACATAAATTGGGATCCGTAAAACCAGGTGCCATGCTACTTGATGCTTCTAAAGAGTATGAGAAAAAAACTGTTCGAGTTGATGAATACatgaaaacaattaaagaTCACTTATTAGAAGCAGTTCAGGAATGCATTAAAGCTGCAGGATATGAGTTTGAACCTAAGAAACAAAGGCGcttaataaagGCTGCCTTATttggaaaaagatttttgcaaGATATGCGTCCTCAAGCCTTTGTTGACATGTGTCAGACAATTAGAGTTTTAAACAACATTCGTGACTTCAAAATTGGGATTCCAATCACTTATGATCaGCTACAGAGGCTGACTACTCCTGTTCTAATAGACAGGTTGATAGCAAGGCGTTTGTACCTCTTAGCTATCAAAATTTGTGACTATCTTCATGTTCCAAAAAGGGAGGGAGCTAGCAGAATTCTTGCGCACTGGGCATGTTACAAGGTTCTACAAGACAATAATGCAGATGAGCTGGTAGCTAAAAGTATTGCAGAAAAACTAGGGGATACCCCAGGGATCTCCTACACAGAAATAGCATTAAAAGCATTTGAGAAAGGAAGAACTGCACTTGCAATGAAGCTTTTAGATTATGAAGCCAAGGCCGCTGATCAAGTTCCTTTGCTAATGAAGATGAAAAGCAATGAACAAGCTTTACAGAAGGCTGTACAAAGTGGTGATACTGACCTTGTGAATATGGTTACTGAAGATATGCGAAAAAGCATGACAACTGGTgagtttttaatgaagatcAGGACATTCCCTTTAGCATTGAGCTTGTTCATAAAGTACTGCAAGAATGAAGAGCATCGCCTACTTATTGATATATACTACCAAGAAGATATGTTTAGTTGCAGTGGAAATGTATTTGTGCAAGACAGTTTTGCTGAGAAAATGTTGGATTCAAGAATAAAGATGCTATGGAAAGCAAAGGAATCATTTGATAAAGGCTGTGTGTTATTTTCCTCACAGgtcactgatgaaaacataaaactacTAGAGTTTCAAAGTAAATTGCAGGTCCAACTTGGAAAACAATTCTTAAATCTTTCAGTTACTGATACACTATACCAACTGCTTTACCAAGGTATTAATAAGCAGGCAGAACAACTACGTAAAGACTTCCTGATTCCTGAATCACGATACTGGTGGACAAAAATACAGGCACTTAGTGCTAACCGAGATTGGGTTGaacttgaaaagttttccAAGTCAAAAAAATCACCAATAGGCTATGAGCCATTTGCAGAAGTCTGTATAAAATATGGAAATAACCTAGTTGAAGCTGAAAAGTACATTATGAAAGTCCCTCttgagaaaaaagttaagCTTTACCTGAAATTAGGaagtCTTGAACATGCAGCAGAAGCAGCATTTCAGACAAAAAGTCTTGACAATCTCAACCTGGTGAGTTTGAAATGTACAAATAACAGAAAGATTGCAGAAAAAATTATGGTCTACCGTTCGCAGCTCTCACAAAAGCAATAG

Transcript

BRAKERKRET00000001633

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9H269	Vacuolar protein sorting-associated protein 16 homolog OS=Homo sapiens OX=9606 GN=VPS16 PE=1 SV=2
Q5E9L7	Vacuolar protein sorting-associated protein 16 homolog OS=Bos taurus OX=9913 GN=VPS16 PE=2 SV=1
Q920Q4	Vacuolar protein sorting-associated protein 16 homolog OS=Mus musculus OX=10090 GN=Vps16 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001418 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04841 all species →	Vps16_N	Vps16, N-terminal region	Repeat	Interproscan
PF04840 all species →	Vps16_C	Vps16, C-terminal region	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006926 all species →	Domain	Vps16, N-terminal	Interproscan
IPR006925 all species →	Domain	Vps16, C-terminal	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR016534 all species →	Family	Vacuolar protein sorting-associated protein 16	Interproscan
IPR038132 all species →	Homologous_superfamily	Vps16, C-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12811 all species →	VACUOLAR PROTEIN SORTING VPS16	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003779 all species →	Molecular Function	actin binding	Interproscan
GO:0005765 all species →	Cellular Component	lysosomal membrane	Interproscan
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0007033 all species →	Biological Process	vacuole organization	Interproscan
GO:0016197 all species →	Biological Process	endosomal transport	Interproscan
GO:0030897 all species →	Cellular Component	HOPS complex	Interproscan
GO:0042144 all species →	Biological Process	vacuole fusion, non-autophagic	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
K20180	VPS16; vacuolar protein sorting-associated protein 16	-	Membrane trafficking	ko04131	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001633.1 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

9TPM > 0

7Conditions

5.9Max TPM

1.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	1	0.27	4.94
Whole	6	5	3.43	5.91
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	1.14	1.14
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	1.40	1.40
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.78	0.78
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
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	4.94
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
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
SRR21134064	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
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	5.91
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	4.57
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	4.57
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	2.94
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	2.59
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	1.14
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	1.40
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.78
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.