Gene detail

Detailed information of BRAKERKREP00000026503.1 in Hydra viridissima

Genomic Location: QPEY01002049.1:364702...388072
NR annotation: XP_047135005.1, Hermansky-Pudlak syndrome 3 protein homolog isoform X2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000026503

atggtgcgAACATTTTTATGTCATACTTTCAAAGAGCCAAGTTCTTTCAATGATAATTATGAGCCTACAGCTTTATGGTGCCAACGTAACTCTCATATGTTTATAGCATCATCAAATGGTAACATACACATCTACAATATTGATAAAGTTGGATGTCCAAAAGAACACAACTTTACCAGTTCTGGTGTTGTTCTGAAAATGGAGTATTGTGAAAAGGAAAAGTTTCTTGTAACATTGGAAGCTAAATTGGTGGAATATAAAAAGGGGATAACAGCAAAGAGTGTCGCATGCCAAGTCcgagtttatttaaatttacatttaagtaTACCATACCGAGTTTACACAACAGTTACAAATGGATATTCAAATACCCTAGATTCATATGATTGCAAGTTCACTATTATTGATCTTTGTTTATTGAATGGAGTTTGTGATATTTctctttgcaaaataaaaagtaatatagctGCTGCTAGTGGAAGCAAAGTCcatatatttgcttttttgaaaaaatctattaacaCAAATAACACTGTGGTTGATTTTTATCCATTACTTGAAATCGAATGcaagtttaaaattcaaagtgTTTCGCTTTACACCAACTGGTTGGCATTTTCATGCAGCAATGAACTGCGAGTcatccaaatatttttaaataatgtagaTGATGGAAGCATATACTTAGGTGAAGATGTTTCTGAACTTATAGAcaaTACGCATGAAGACCAAGTTAACTCCAGAAATCAAAATGACAATTATTCTTCTGAAGATGAATTAATTGTTTGGAATTTTGATCAAGGTGCTGATGGTGCAAGAGCTACATCATTTTctataaacaataaaagagtatttttaagtaagcaaaatgaaaattacattTGGGATAGCGAAAATAGTGTTATAAATTTAGATCTGATTAAAGATGAACAGCCATATGTTGACAAAGATTCTTCTTCTAAAGAAGTGTcaggttGGATTGAAGAACTAGTTGGTCATCCATTGCGAGTAATAGCACTTAGTAATGAACAGCCCTCTTGTATCACACGCTTATATCGAAGATTTGAACCTtctgaaatttcttttgatgatATGGTAGATCACCTGCACAGTTTGCAATGGCTGCCTGTCTTTACAAAtgaaagcatAGACACTCCAACAAATGAAATGGATATGAATCAGACAAACAACTGCCTTAAGCTTCCTAGTGGTTTTTCATTGTTGGCcttggctttttttttctccactGGAAAACATGGTTTTCTTTATGACTTcacaaatataacaaaaaatatagctGTTTATAGTTATGCTTCAGATTGCTTTTCTGCAGAACACACAGCATCTTGCCTTAacattgtaacaaaaaatggtCTTGAAGTATATTCATCACGATTATATGCATTAGCAGCTGATCATTATCatagtttgaataaaactGGGAAAGAACAACAGCAAGAAATGAAATCTTCACAAAATGAGAGCAGGAGTTTAAGCAATAGtgatttgaaaatgaatgatGAACCAATAAGTTGTCAAATGCCAGATATTGAAAGATTgtcttatcttttttatgactCAAAATATCTTCTATCTCCTTGTACCTGGAATGATGTTGACTTGTGTTTGGTTGGATTTTATTCTTTGTCCAATATCTATTTAGCATCTTCATCTGTATCTAAAAGAGTTTTTCTCGTGAAAGATCAGTCCAAgtCAAAGAAAGTTACTTGCAGTATTTCTTCATGGAATGTTTTTGTTATGGCAAAACCATCTGTGTCATCTATATATGAGAACATTATGCGATTTATAAAAGGTAGCGAGTTAACTAATCCATCAGTTTACTATCAGCTATTAAGTGAAGCTCACTTGCTTGTGCGTTCTCATTTGTATTGTGGTATTAATAATGatgagaaaagaaatttactttcTCTGATGAAAGATTCAGCTTTGAAGCTTgcagatttctttttatgttgtGATTCTACTTTTGGCTATTATTCCCAAGTGTCAGAATTTTCTAATTTGGCTGAAGTTAGTTTTGAACAAATACTTAAAGGATTAATTTTGGAACCAAAATTGagCTATGGTCCAGGAATGATTGtttatttgaatgaaatgGTATTTGGTGACAAAAAGTTGTATCTTGAAAAAgaaGTCATAACATTTGTCCTGGACATATACCTGAACTATAAGCCTTCTTTATTATCAAAAGTCTTTTTTGATTCTCAATTGCAAAATATACAATCAGATCTTGCTTTGGATTACTTAACAAAGATGAAGTTCAAAACTGACAGCAGaTTAAGACCATATGATTATTTATGCTTTGCTATTTTAAACATGGAGCTTGGAGATCCAGCCCATGCTGAAAGTTGGCTCAAAGAGATGCCTGAGgaCTCTCTGATTACAGTATGCATTAAGAATTACAATTTGTTATCACATGATTTTACTTCTCCAGTTGGCCAGCTGTTACAAAAGAGATTTAAGCTTGTATTCACTAAGATCCTTGTTTCTTTATTTGGTGCTGGTAAAATTGATATCAATACTATCTTGAAGATTTTTCAGaaaaataaaaatggacaAATGGTTTGTAGCTTCAATGTATGCAGTGTCTTAGAAGGCATTTTAAATGatggcaattatcaaaatcatttcttaGATGTTGCTGTACTTTTAATCGATcaatacttaataaaaatgtctaaaagtCATTACTCTGAAAAATGGCAAACTAGTCACCAGCATATACCAAAAGGAAATGGTCATTTTGCTGTTCGCTTCAAATGGTTGGACTCAATGCTACCATTTACAGGAGATCCCCCGTGTTCTCAAGattgtatttttaagcaaatggCTATCAAAAATGCTTCAAAGTATGAAAATCAAGTTTCTTCAAATCTAACAAATCCAAAccaatatttacaaagtttgtCTTTTTCTATTGGTAAAGGTATCAACCTCgaagattcaaaaaatgtgaatTATTGTCCGTGCTGTTGTTGCTGTGAAACTTTGCTTAAACTTCAGtctATTTTATGTTCGAAATACTGTAAGAAACAACTAGCAACGAGTGTCTTGCAAATGCTAGataaatattcatttgttGGTAAAGATACTCTGTTGTTGCTCTGTTGGCCAAAAGTGGATTTTATCAGAGAGGCTGCAGTTTATTTAATGGCGAACTACGTTGATATTACTGTCCAATACGCCAATGATGTTTTTGATTGGAAAGCGCAaTGGCAGACACTTCTTCAACATGtatttgaattattaaaaaacgatGACATGGTGTGGAACAAGCAAGCTATTTTAGGAGTACTTCGAGgtgTTTTACATCGTCTTACACGAGCATACTCTCCCCTcgagttttttgattttttgccTCGCGATGGTAACCTTCAGTTCTTCCTTCCATTCATTCTTGAATGCTGGTTTTTCACAAAAGCAAATCTGCTGAAACGAGAAATGGTGAGTAAATATCGCTTATTGGAATCATCATCTTTAGAAGCGTAA

Transcript

BRAKERKRET00000026503

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003955 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14763 all species →	HPS3_C	Hermansky-Pudlak syndrome 3 protein, C-terminal region	Repeat	Interproscan
PF14761 all species →	HPS3_N	Hermansky-Pudlak syndrome 3 protein, N-terminal	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR029438 all species →	Domain	BLOC-2 complex member HPS3, C-terminal domain	Interproscan
IPR029437 all species →	Domain	BLOC-2 complex member HPS3, N-terminal domain	Interproscan
IPR017216 all species →	Family	Hermansky-Pudlak syndrome 3 protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR28633 all species →	HERMANSKY-PUDLAK SYNDROME 3 PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006996 all species →	Biological Process	organelle organization	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

No KEGG orthology assignment for BRAKERKREP00000026503.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000026503.1 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

13TPM > 0

7Conditions

58.0Max TPM

15.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	3	4.62	34.10
Whole	6	6	45.07	58.04
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	35.21	35.21
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	29.33	29.33
symbioic hydra M9 strain · symbioic hydra rep1	1	1	14.91	14.91
symbioic hydra M9 strain · symbioic hydra rep2	1	1	13.70	13.70
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	34.10
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	27.85
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	21.20
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
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
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	58.04
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	45.99
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	45.54
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	43.60
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	40.83
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	36.43
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	35.21
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	29.33
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	14.91
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	13.70
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.