Gene detail

Detailed information of BRAKERKREP00000001667.1 in Hydra viridissima

Genomic Location: QPEY01000004.1:643526...650872
NR annotation: XP_047129027.1, WD and tetratricopeptide repeats protein 1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000001667

atgttttcacagTGTAAGCAAAGAAATATTGCAGTGTGTTGCAAGCAAAGGGAAGTAGAGcaaattggtttaaagaagtttgaaaGAGATATTCAAGTTTCATTTCCTTTTGTTAAAGCTATTGGGTTGGAAAAAGAGTTAGAGATTGTTTTCATCTTTGAAGCCCATATACTTATTCTTAACTATTTAGTATCTGGTTCTGATGATACTCAGATTATTCTTTGGGATATCAATAAAAGGAaagcaaacataaaaatatcaacaagtCATGAgggaaatatattttctgtCAAGTTCTTACCTTATTCTTCCAATAACATTGTTGCATCTTCTGCAGCTGATAGAGTTGTTAATCTATATGATGTGTTCACACAGTCAGAAATCCATTCATTCAAATGTCATTCAGGAAGAGTGAAAAAATTAGCTGTATCAAGTCACCTTCCATTTTTACTTTGGAGCGGTTCTGAAGATGGTTCTGTCAgCTATTTAGTATCTGGTTCTGATGATACTCAGATTATTCTTTGGGATATCAATAAAAGGAaagcaaacataaaaatatcaacaagtCATGAgggaaatatattttctgtCAAGTTCTTACCTTATTCTTCCAATAACATTGTTGCATCTTCTGCAGCTGATAGAGTTGTTAATCTATATGATGTGTTCACACAGTCAGAAATCCATTCATTCAAATGTCATTCAGGAAGAGTGAAAAAATTAGCTGTATCAAGTCACCTTCCATTTTTACTTTGGAGCGGTTCTGAAGATGGTTCTGTCAgAGAGTTCGATTTAAGAGAACCCTACCACGAATGCTCTTCCTCAtgttctaatatttttataaatctcaGACAACAAGTAATGCTTACTAGTGAAGTCAAATGTATTCAAGTTCATCCAACTCATCCAGAACTCATTGCTGTTGGTTGCAATGATGCTTATCTGCGTCTATTTGACAGACGAATGGTAAAGCAGAATAGAGCAACAAATTCAACTTTATTCGAAAATTGTGTGGATTATTTTGCTCCAGGTCATTTACTTCCTCGAACTTCAAAAGTTTCTAAGCGAAGATTGTTTGTTACAACTCATCTAGCTTTCAGTCCAAATGGAGCAgaaattcttcaaaatcttGGAGGAGATCATATATACTCATataatttacttgaaaaaaaactttcttttaagttaaaagctCCTTGTGATAAAAATTGTGCAACATCTAATGAACTTCAACATAACTTCAAAGCAAGTGCAAATAATATGTTGAGTTCTACTTATACTACCAGACAATCACCACCAAATATTATAAGCAGTGATATTTCACGTGATAAAGCAATGAGCTTTAAAGTTAAAGGAAATgaagcattttcaaaaaaaaattactatcaAGCTGTTATTTACTACaatgaagcattaaaaatttacccaAGCAATTCAGTTTTATTGGCAAACAGAGCGGCTGCTTTGCTTCAGCGCAAGTgGAACGGTGATTTATATTCATCTTTACGCGATAGTGAAACAGCTGTGGCTCTTGACCCATTGCATCATAAGGCCTTCTTGAGACAAGTGAAATGTCTTCAAGAATTAAAGATGCATGAAGATGCTTTAAAATGCTTTGActtgtttaaagaaaagtttccaGAACAAGCAGAAAGTGGTACTGCTAAGCAATTAGAGGCAGATATAAGAAAATctatcattacaaaaaaagcagatTCAGATAATGATCATGGCGTTTATCTGCCtgaatacaaatttaataacaaagaaGAACTTTCTAGGCGGGAAAAATCTTATGATTACTCAACTCGTTTTGTTGGTACATGCAATATAACAACAGATATAAAGGAGGCAAATTATTTTGGTAGCTATGGCCAATATATTGTTGCAGGAAGTGACTGTGGATGCATATTTATTTGGGAACGAGCAACTGCTAATATTGTGAAAGCTTTGCGTGGTGATGAGTCTATTGTTAACTGTTTACAACCTCATCCAACAGCTTGCTTAATTGCAACAAGTGGTATTGATCCAGTTGTACGCCTGTGGAGTCCACAATATGATTCAAAGAAACTAacacaaaatactcaaaatttAGTATGCTCTAATCAAACAAATATGAACTCTGATCCATTAGATGAAATGCTTAGGACTATGGGATATATACCTACACTATCAGATGGTGATGAAAACGATGAACCACGTGTTAATTGTGCTACaagttaa

Transcript

BRAKERKRET00000001667

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8N5D0	WD and tetratricopeptide repeats protein 1 OS=Homo sapiens OX=9606 GN=WDTC1 PE=1 SV=2
Q80ZK9	WD and tetratricopeptide repeats protein 1 OS=Mus musculus OX=10090 GN=Wdtc1 PE=1 SV=1
Q94BQ3	Protein ALTERED SEED GERMINATION 2 OS=Arabidopsis thaliana OX=3702 GN=ASG2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007823 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	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
IPR045151 all species →	Family	DDB1- and CUL4-associated factor 8-like	Interproscan
IPR019734 all species →	Repeat	Tetratricopeptide repeat	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15574 all species →	WD REPEAT DOMAIN-CONTAINING FAMILY	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:0045717 all species →	Biological Process	negative regulation of fatty acid biosynthetic process	Interproscan
GO:0080008 all species →	Cellular Component	Cul4-RING E3 ubiquitin ligase 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
K11807	WDTC1, DCAF9; WD and tetratricopeptide repeats protein 1	-	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001667.1 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

9.2Max TPM

2.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	1	0.29	5.16
Whole	6	5	7.04	9.23
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	5.54	5.54
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	6.64	6.64
symbioic hydra M9 strain · symbioic hydra rep1	1	1	4.52	4.52
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
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	5.16
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
SRR21134060	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	9.23
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	8.48
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	8.46
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	8.14
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	7.93
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	5.54
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	6.64
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	4.52
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.