Gene detail

Detailed information of BRAKERKREP00000012987.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047140481.1, AP-3 complex subunit beta-1 isoform X1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000012987

atggCTGGCTCTTCTGCTGTGTCTTACAACAATAATGATGGAATGCCAGCTCTTTCTGTTGGTCATTCTATATATCCTACCAGTTCTAGCAGTTCTAATACAGCACAATCAGTTGTTTCATTTATCACTGgacattttggaaaaaagcatgatgatttaaaagtaatgctTGATAGTTCAAACAACTCCCAAAAATTAGATGCCATGAGGAGAATTGTTGgaATGATGGCCACTGGAAAAGATGTGTCTGAATTGTTTCCtgctgttgtaaaaaatgttgtctgtaaaaatattgaggtaaaaaaattggtcTATGTTTATTTGGTGCGTTATGCAGAGGAGCAACAAGATCTTGCTCTTCTTTCAGTTGCTACTTTTCAAAGAGGACTAAAGgatcCTAATCAGCTGATTAGGGCAAGTGCCTTGAGAGTCTTATCAAGCATTCGAGTGCCTATGATAGTGCCTATAATGATGTTATCTTTGAAAGAAGCTGTTACTGATTTGTCTGCATATGTTCGAAAAACAGCTGCTAATGCTATTCCAAAGCTTTAcagtatggATCCAGAGCAAAAAGATGCTTTAGTTGAAATCATAGAAAAACTACTTCAGGATAAAACTACACTTGTTGCTGGAAGTACAGTTATTGCATTTGAAGAAGTTTGTCCAGAAAAAATCGATTTAATACACAAAAACTATCGCAAGCTCTGTAACATGTTAATTGATATTGATGAGTGGGGCCAGGTGGCGGTGATTAATATGTTGGTTAGATATGCACGCACACAGTTTTTGGATCCAAATAAGAATGTTGTACCAGGCGTGGATCAAAAGTTTTACCCTTCTGAATCTGAAAAGAGTGATTCAGAGGAAGAAGAAGGTAAAAGTCCTAAATCTAAAGCTTTTTCCATGGATCCTGATCATCGATTGTTACTTAGATCATGTCAACCACTGCTGCTCAGTAGAAACTCTGCGgTAATAATGGCAGTAGCCAAGCTGTACCACCATATTGCACCTTCATCTGAAGTTGGAGTGGTAGTAAAAGCATTGATTAGGCTCCTTCGAAGCCacagGGAAGTTCAATCTGTAGTTCTAAGCAATATTGTAACACTGTCACTGCAAAGAAagggtttgtttgactcatatttaaaatcattctttGTGCACACAGGAGATCCTActcatataaaaaagttaaagctcgaaatattaacaaatttagcAAATGAATCAAGTATTCCAACTATTTTAAGAGAATTTCAGACATATATTGCAAGTTCTGACAAAGAGTTTGCTGCTGCAACTATCCAATCTATAGGTAGATGTGCATCAAATATTCCTGAGATAGCTGATACATGCTTAGCTGGGCTTATCCGGATGCTCTCAAACCGAGATGAAAATGTTGTAAGCGAGAGCATTATagtgattaaaaaactgttgcaAATGAGACACAAAGACCACAGTGAAGTTATACCACATATGGCAAAACTTCTTGATAAGGTTCATGTGCCAATGGCTCGAGCCAGCATATTATGGTTGATTGGCGAGTATTCTGATCGTATACCAAAAATTGCCCCTgatgttttgagaaaaatggcaaaatgtttttcatcagAGGAAGATGTTGTAAAGCTTCAAATAATCAATTTGGGGGCTAAACTCTATATTACCAACTCAAAACAGaccCGCACACTTTGTCAATATGTATTTCAGCTTGGTAAATATGATCAAAATTATGACATTCGTGATCGAAGTcgttttcttaaatttcttttatttcctgCTGATAAAACAGAAggTGCTAACAAtcttaagaaaaaagcaaaaaaaatattcttaatagAAAAGCCTGCTCCAGTGCTGCAGTCTTTATTTAAAGATCGTGGTCAATACCAATTAAGCTCACTTTCTCATATGATTGATTCAATTGCAAATGGCTATCAAGAATTGCCAGAATTTCCAGAAGAACAGCCTGATCCTAACGTACGAAATGTtgagctcgaaatattaacaaatttagcAAATGAATCAAGTATTCCAACTATTTTAAGAGAATTTCAGACATATATTGCAAGTTCTGACAAAGAGTTTGCTGCTGCAACTATCCAATCTATAGGTAGATGTGCATCAAATATTCCTGAGATAGCTGATACATGCTTAGCTGGGCTTATCCGGATGCTCTCAAACCGAGATGAAAATGTTGTAAGCGAGAGCATTATagtgattaaaaaactgttgcaAATGAGACACAAAGACCACAGTGAAGTTATACCACATATGGCAAAACTTCTTGATAAGGTTCATGTGCCAATGGCTCGAGCCAGCATATTATGGTTGATTGGCGAGTATTCTGATCGTATACCAAAAATTGCCCCTgatgttttgagaaaaatggcaaaatgtttttcatcagAGGAAGATGTTGTAAAGCTTCAAATAATCAATTTGGGGGCTAAACTCTATATTACCAACTCAAAACAGaccCGCACACTTTGTCAATATGTATTTCAGCTTGATCGTGGTCAATACCAATTAAGCTCACTTTCTCATATGATTGATTCAATTGCAAATGGCTATCAAGAATTGCCTGAATTTCCAGAAGAACAGCCTGATCCTAACGTACGAAATGTtgagATGGAAACAGTTTATGGAAACCAGTTCCTTTtgactaaagaaaaaaatgttacatctCCAGATGCAAATGATAAAAGCTTTTACTCATCAGAAGACGAggatgaagatgaagatgaagaagacAGTGGAGAAGAAAGTAGCTCATCAGAAGATGACAAGAACACTGAAGATGAAGAGTCATCTGAAAATGATTCTAATGAAGAGAAAGAAGATTCTGGTGAAGAGAGTGAGTTTGAGGAGTTATCTGAAAGCGAAGAAGAAAAGGATAATACAATAGACATAACTAAAtcttctgaaaataaattgtcagGTGGAAGTAGTGAAGAAGAAACTTCTGATGAAGAAAGTGAAGAGGAAAGTTCTGAAGAGGAAAGTGAAGAAGAAGAATcagatgaagatgaagatgaagtAGTTGTGCAAGCACCagcaaacaataaaattgaaaaaatcaggAAAAGTATTCAGCCAAATCAAAAATCCTATGATCAGCTGCTTGACTTAGATGacttttcagttCCATCAAAGCCTAATACAGTTGACACTATTAAACCATCGTTGGTTTCAGATATGGCGAATCTATCTGTTGATCCTACAAATTGTACTACCATATCCTTACAGTCTTCTcCTAGAAACTTCAAGTCTTTTGAACTTCTCAGCAAAATAAATGGCAAGGGTTTGATAGCATATTACAAGTTTCCTCGTGCACCTTGCATATATTCAAGTACCATGGTTGCCATTGAAATAGAGTTTGAAAACTCAACCAATACTGAGATCAAAAGATTACGAGTTGAAAACAAGaaattatcaTCAGGAGCTCTTATGCAGGAGTTCAATGAAATtgCAAGTATTCCAGCTAAAGAGAGCATATTAGCTATGGTTGGTATTGACTTCAAGGATACTGTTCAACCTGTGACCTTTGATCtatgcactGAATCTGGAAAGTTCAcagttcaaataaaagttcCTGTTGGAGAGCTGATGAAAGGAGTTTCACTAACTCAGCAGGAATTTACTACACAGCAAAAAAAGTTGACTGGTATGACAGAAAGTAAACTTTCCTGCCAACTTTTCGATCCcgttcatattttaattagtaaaacaGCAGAAATAGCTAATATGACTCAATCGCCTTCCCCTCTTGAAgatcaaaatgttttcaggTTTGCTGCCAATTTAGTTTCCTCTGGCTTACCTGTTCTCctttctgttaaaaatgatgGGAGCAATAGTCAGATTATTGTTAATTGTGAAAAGATTAGCATCGGATCATTacttgtaaaagaaataaaaagtgcaatatcacgttaa

Transcript

BRAKERKRET00000012987

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7YRF1	AP-3 complex subunit beta-1 OS=Canis lupus familiaris OX=9615 GN=AP3B1 PE=2 SV=1
Q32PG1	AP-3 complex subunit beta-1 OS=Bos taurus OX=9913 GN=AP3B1 PE=2 SV=1
O00203	AP-3 complex subunit beta-1 OS=Homo sapiens OX=9606 GN=AP3B1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003541 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF14796 all species →	AP3B1_C	Clathrin-adaptor complex-3 beta-1 subunit C-terminal	Family	Interproscan
PF01602 all species →	Adaptin_N	Adaptin N terminal region	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029390 all species →	Domain	AP-3 complex subunit beta, C-terminal domain	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR002553 all species →	Domain	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Interproscan
IPR026740 all species →	Family	AP-3 complex subunit beta	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR026739 all species →	Family	AP complex subunit beta	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11134 all species →	ADAPTOR COMPLEX SUBUNIT BETA FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030117 all species →	Cellular Component	membrane coat	Interproscan
GO:0030123 all species →	Cellular Component	AP-3 adaptor complex	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
K12397	AP3B; AP-3 complex subunit beta	-	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 BRAKERKREP00000012987.1 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

16TPM > 0

7Conditions

183.2Max TPM

73.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	6	33.14	126.70
Whole	6	6	174.29	183.24
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	124.20	124.20
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	141.16	141.16
symbioic hydra M9 strain · symbioic hydra rep1	1	1	116.88	116.88
symbioic hydra M9 strain · symbioic hydra rep2	1	1	104.94	104.94
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	126.70
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	110.72
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	105.27
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	103.97
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	87.06
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	62.75
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	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
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	183.24
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	182.16
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	177.39
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	175.20
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	165.14
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	162.59
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	124.20
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	141.16
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	116.88
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	104.94
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.