Gene detail

Detailed information of BRAKERKREP00000001337.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047126355.1, coatomer subunit alpha-like [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001337

atgttgaCTAAATTTGAGACCAAGTCTGCTCGTGTTAAAgGTCTTGCATTTCATTCAAAGAGACCATGGGTGTTGGCAAGTTTACACAATGGTGTCATACAGCTCTGGGATTATCGAATGTGTACTCTATTAGATAGATTTGATGAGCATGATGGTCCAGTACGTGGAATCGATTTTCATGAGCATCAGCCTTTATTTGTTTCAGGTGGTGATGATTATAAGATTAAGGTTTGGAattacaagcaaaaaaaatgcatatttacATTGCTAGGTCATTTGGATTACATCAGAACTACATTCTTTCACAATgaatatCCTTGGATAGTAAGCTGTTCTGATGACCAAACAATACGTGTTTGGAATTGGCAGTCAAGAAATTGTATCAATGTTTTAACTGGACACAATCATTATGTGATGTGCGCACAGTTCCACAAAACAGAAGACTATATTGTTTCTGCTTCTCTTGATCAAACAGTGCGTGTATGGGATATTTCTGGTTTgcgaaaaaaatttgctgCCCCTGGTACTAAAGATCGTGATGATACATCAGTAAAAAGTCCTGGACAAATAGATTTATTTGGTCATGCTGATGCAGTTGTGAAACATGTCCTTGAAggTCATGATCGTGGGGTAAACTGGGTGACATTCCATCCTACTATGCCATTAATTGTATCTGCAGCGGATGATCGTCAGGTTAAATTATGGAGAATGAATGaatcaaaaGCTTGGGAAGTTGATACCTGTCGTGGTCATTACAATAATGTTTCATCTGTACTCTTTCACCCAAGACAAGAGTTAATTCTTAGTAATTCAGAGGATAAATCCATACGTGTTTGGGATATGTctaaaagAACTGGAGTCCAGACTTTCCGCAGAGAAAATGACCGATATTGGATACTAGCTGCTCATCCAACTCTCAATTTGTTTGCTGCAGgacATGATAGTGGCATGGTGGTTTTTAAACTGGAGCGAGAAAGACCAGCTTACACTGTTTATCAAAATACTCTATACTATGTTAAAGATCGTTACTTACGAGTATATGAATTTGGTTCTTCAATTGATAAGCCCATCATGCAGTTTAAAAAggGTGCTGGTCGACCAAATCCAGTTAACTTGGTGTTTAACCCAGCTGAACAATGCATTCTTTTAACCTATGGCACAAGTTCATCAGTAGACAGCCAGGTCTATGAGTTGCATGCTCTTCCTAAAGACATAAAATCCTCTGATCCTGAAGTTTCTGAAGGAAAGAGAGCTGCTGGTGTATCAGCTGTTTGGGTGGCTCGTAACCGCTTTGCAGTCCTtgataaacaacaaaatgttgtcattaaaaatttaaaaaatgaagtgaCAAAGAAGGTTACAACTCCTTCATGTGACATGATATTTTATGCTGGTACAGGAAGCTTACTTCTAAGGGATGCTGAGCAAATCATGCTCTTTGATGTTCAACAAAAAAGAGTAATGGCTACCATTAAAATAGCTAAATGCAGATACGTTATTTGGTCATCTGATATGAACTTTGTAGCTTTAGTTGCAAAGCATAttATTTCAATCTGCAATCGGAAAATGGAAAATCTATGTACTGTTCATGAAAGTGTAAAAATCAAGAGTGGTGCATGGGATGACACTGGGGTTCTTGTTTATACAACAAGCAATCATATTAAATACACGTTAACAAATggTGACAGTGGCATTATTCGGACATTGGATTTGCCAATATACATCACAAGAGTAAAGggAAGTAGTGTTTATTGCTTGGATCGGGACTGCAAGACAAAGGTTTTGAATATTGATCCCACTGaattcaagtttaaattaGCTTTAGTAAATCATAGATACGATGAAGTACTACATATGGTGCGAAATGCAAAGTTGGTTGGACAGTCTATCATCTCTTATTTACAGAAGAAAGGCTATCCTGAGgttgcACTTCACTTTGTTAAAGATCAAAAAACAAGGTTTGGTCTTGCATTGGAATGTGGTAATTTAGAAGTTGCATTAGAAGCTGCAAAATCTCTTGAAGACAAAGTTTGCTGGGAAAAGCTTAGTGAAATGGCTTTGAAGCAAGGAAACCATcagGTGGTAGAGATGTGTTatcaaagaacaaaaaattttgatcgtctttcatttttatatctaacAACTGGTAACACTGACAAGTTAaggaaaatgttgaaaatttctgaaattCGAAAAGATGTAAGTGGTCATCTTCACAATGCTTTATACTGTGGTGACATCAGAGAAAGAATTAAAGTACTGAAGCAAGTTGGTCAagGTTCCCTAGCCTATTTGACGGCTGCCACACATGGACTGACTGATGAATGTGCTGAATTACAAGCTACATTCAACTTGGATCCAGAAAAGCTACCAGCAATAAATCCTAATGCTAAATTGCTCCGACCTCCTGTACCTATTTTACTGAATGAAGGCAACTGGCCATTACTAGCTGTTAGTAAGACGATATTTGAAGGATCCTCATCTTTGAAAGATGGTGCAACAAGTAACTTGTCAGTCTCTGCTCCTCCTCAAGCTGATTATGGTGAAGAAGGAGAAGGTTGGGGAGATTCAGATCTTGTATTGGaagaagATGCAGGATTTGGTGATCCTgatgagaaattaaaaattgatgaagGGAGTGGCTGGGATGTTGGAGATGATGATCTTGAACTTCCTAAGGATCTGGAAGTTGCTCCAGTATCAGGTGGTGAAGACTTTTATGTTCCTCCTACTAAAGGCAATAGTCAAGGGCAAGTATGGATATCCAATTCACAATTGCCAATGGATCACCTAGCTGCTGGCTCATTTGATTCTGCTGCAAGGTTGTTAAATGAACAGTTGGGAGTTGTGAATTTTGAACCTTATAAACAGTTATTTATGCTTGCATATGCTCGTGGACGTGTGGCTGTACCTGGTCTACCTTCATGTccaagtttatatttttatccgCATAGAAACTGgaaagaTGCTGGTGCAAAGGCAGGATTACCAGCTGttggtttaaaattgaataacttAGTCCAACGTTTACAGGTAGCTTATCAACTGACAACTGGTGGAAAGTTTGCTGAAGCCGCAGAAAGACTTCATCAGATTCTTCTAAGTGTTACTTTGTTAGTTGTAGAATCAAGACAAGAAATAACCGAGGCACAACAACTTTTGGGAATATGTAGAGAATATCTTGTTGGTCTTCAAATGGAAACTGTTAGGAAAGATTTACCCAAGgaCACAGCTGATCAACAAAAGAGAATTTGTGAGaTGGCGGCTTATTTCACTCATTGCAGTTTGCAGCCTATTCATTTGGTGCTTACGTTACGGACAGCTCTAAATCTTGCTTTTAagatTAAAAACTACAAGACTGCGGCCTCTTTTGCACGTCGTTTATTAGAGTTGGGTCCAAAACCTGAAGTTGCTCAACAGacACGAAAAATTTTACAAGCCTGTGAAAAGAACCCCATTAACGCGGTGGTATTTGATTACGACGAACTTAATCCGTTTTCAATTTGTGCTGTTTCGTATTCTCCAATATATAGGGGGAAACCTGAGGAGAAATGCCCATTATGTCAGGCTTCGTACAAACCGCAGTACAAAGGAATAATTTGCAAAATATGCGAGGTTGCTGAAGTCGGAAGGCCTAGCTCTGGTTTGAAAATAAGTCTTTCGCAGTTTCGCTAA

Transcript

BRAKERKRET00000001337

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P53621	Coatomer subunit alpha OS=Homo sapiens OX=9606 GN=COPA PE=1 SV=2
Q27954	Coatomer subunit alpha OS=Bos taurus OX=9913 GN=COPA PE=1 SV=1
Q8CIE6	Coatomer subunit alpha OS=Mus musculus OX=10090 GN=Copa PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004966 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04053 all species →	Coatomer_WDAD	Coatomer WD associated region	Repeat	Interproscan
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF06957 all species →	COPI_C	Coatomer (COPI) alpha subunit C-terminus	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR016391 all species →	Family	Coatomer subunit alpha	Interproscan
IPR006692 all species →	Domain	Coatomer, WD associated region	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR050844 all species →	Family	Coatomer complex subunit	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR011048 all species →	Homologous_superfamily	Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily	Interproscan
IPR010714 all species →	Domain	Coatomer, alpha subunit, C-terminal	Interproscan
IPR047312 all species →	Domain	Coatomer subunit alpha, WD Associated Region	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19876 all species →	COATOMER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0006888 all species →	Biological Process	endoplasmic reticulum to Golgi vesicle-mediated transport	Interproscan
GO:0030126 all species →	Cellular Component	COPI vesicle coat	Interproscan
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030117 all species →	Cellular Component	membrane coat	Interproscan
GO:0006890 all species →	Biological Process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	Interproscan
GO:0006891 all species →	Biological Process	intra-Golgi vesicle-mediated transport	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
K05236	COPA, RET1; coatomer subunit alpha	-	Exosome	ko04147	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001337.1 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

8TPM > 0

7Conditions

13.9Max TPM

2.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	1	0.58	10.43
Whole	6	4	7.90	13.89
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	3.70	3.70
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	3.27	3.27
symbioic hydra M9 strain · symbioic hydra rep1	1	1	2.05	2.05
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	10.43
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	13.89
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	12.85
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	11.28
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	9.39
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	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	3.70
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	3.27
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	2.05
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.