Gene detail

Detailed information of BRAKERKREP00000012491.1 in Hydra viridissima

Genomic Location: QPEY01000063.1:266209...280950
NR annotation: XP_047139617.1, RAB11-binding protein RELCH [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000012491

atggctgaaaaagaaaatggaaagAATTCAGGGTTTAATCAAACTACCACCAAGACACAGCAGCAAGTTGAAGAAATAGATAATGttgctaaaatattattagagAGAAGATTTTTTCTCACCGCTTTAGAACTTCACACAGAATTAATAGAGTCAGGAAAAGGGTTGCCGAGgttaaaagaattcttttcaaatccaaataattttgaattccAAGCTAAAATCGACTCTTTTGCTCTTTTACgtaaAGCGCCAAGTGTCTTGACATTAGACTCAATTGATGATTTTGCACGTTACTCTGATGATGATGTACATGAAACTGATGAAAAGATTGCTGTCCTTGAATTTGAGCTGCGTAAAGCAAAAGAAACAATTCATGAACTTCGTCAAACTGTAACTGAAATGACCTCAGaatCAAAAAAGCACACTGTAAATGAAGGAAAGGATTCTAGTGCTAATCAATTTGAACTTcgaactttgaattttttggtTAATGAATATCTTCTGAGATATAACCACAAGCTAACCTCTATAACCTTTGCAGATGAAATTGGTGATCAGGATTTAGATGACTGGGAAGATGTGGGTTTAAATACTGCCCAACCTCCTGATTTGTTGCATTTATTTCGTGATTTTTCGCATCATGTTATAAATCCGGAATCAAGGCATTTAGAAGAACTTCGAGATATGCAGAATGAAGTTGATTTATTGAGTTCAAGATGTGAAGAGCTGAagttgcaaattaaaaaactcaaccAAACCAACAGCAAACTCATGTTTGAAATAGATGAGCTCAACAgGAATCTTATTATTGCAAAAGAAGAAtcagctttaaatttaaaagcttctaCAAGTGACAGCAATTTTGAGAAATCTGATCTTGAAGaaggaaaaaatgtttctgaacTTACTgaacaaaatagtttaaaaactgCAGCAATAAAGACAGGAGAAACTTTGTCTAGTAATGCAGATGAGTTAGAGCAGTATAAAGTTAACATGACTTATCAAGCATCAGATTCTCAGACAGCACTACACTCaacagaaagtttaaaatctttttcaagcTTTGGCAGCAGTTTTGAATTGGAAGAAAACACTAAAGATGAATCTAAGCATGaattttcagcaaaagttCATATTTCAAGGATAAACTGTGGTAGCCGACTTGTTTCACCACTATTCCTCGAAGTGCTTTTTGCAACAGTTAAAGGGAGCGCAGAACAAAGCAGTGCACAATCGTCCACACATTCAAAACAGGTTTCTTACTCAAGCTCTGCATCACCTGTAGAGGTCATAGCTAGTTCACTTCCTCAAATTGTTCCAAatgttttacttaataaacgtgaggAGTTGATTCCACTCATACTGTGTGCTGCTCGATATCACCATGATTCAAAAGTTCGAGATAACCTTCTGCATAtgctttttaatcttattaaaaGACCTGAGTATGAGCAGAGgaaaattattattgatgGTTTTGTTGAGTTTGCTGGCAGTGCAGAATCAGCCCGAATAGAGTCAGAGCTTTTACCTCAATGTTGGGAGCAGataaatcataaatttccAGAAAGAAGATTGCTTGTTTCAGAGACTTGTGGATTTATCTCACCGTACCTTCCAGTAGAAATTCAAGgttcattgattttttctatGCTTTCACAAATGTTGCAAGATGACCGAAGTGAGATTGTTCGTAACTCtgtaattaaaagtttggCAATTGTAATAAGTGCTATTACAGATACCTCTAAATACATGCAGgCTTATTCTTTGTTTGAATGTGGTCTACTGGATATTGTTGATGAGGTTGTTTCAACCACAAAGAACATTTTGTTACCTGCTCTTTCTATGTGGGCATGTGAAATTAACAAACTTCaatctcattttttaacagacCTTTTCAAAAAGTGCAAAATGGCTTTGCAGaattgGCAAGAATCACGCTTATCTGAAAATACTAACGATGCACATATGATATTATTAGAGtctgaaaaaaagtataacaatTATATGGATTGCTTAGTGAAGACAGtatctattttatttgttgactGCATCATAACagGTCCTTTTGAAATATCGAAAGATTGCTCTTCTTTATCAGAGGATCGCCTACCATTcacaaaaaacagtttatttaaTGTGCACACAATTCTGGGAGATGACCTGAAAATTAGTAGGCTAGTCAGACAGTTTGATAGTGCATTTGATGGTGAATCTACAGATGCTTTAACACCCTGGGAACAAATCCAATGGGTTTGTGATgttattcctttttttgaaaagcggATGAGAAATACAGGTGCTGATTTTCTTAACAATACTCCTCCTGTTTGTTCTCCATTGCTAACAGTATTTTTATGTGGTGTCCTTCCTGTCTTTAAAGGGAGTGAACAAGCCGGTCGACTGTGCACATTTATTAAGCAGTGTTTATTGACAATATCAACACAGTGTCTATCTCCTCAGTTtctaattttatcttttaatattttaagCAAAGACAAGTTACATCATACTCCATTACTTGATATGCTACGCGAATTATTAGTTTATCCGGTTTCTGAAGTTCGAATATCTACAGTGTCTCTCCTTGAGGTTTTAGCAAAACACATAAGTAATGAGCTTTTGGTATCTCAAGTTGCTGCAGCAATCATCACACTTACAAATGACAGAGActtGTCAGTTCGTTTAGCTTCTATCCCTGCACTTGTGTGTATTGTTGAAAGTGCACGTGATAAATTaatACTGgataaaatatcattacagTTACAAAACCTACTAGACGATGAACATCTACAAAAAAACActgattttctaaaagttgttgttcaagctattacaaaaatgatttcaagCGCTGATGTTAAATTCAGAGATGAGTTTTTGTTGCCTCGTTTGAAATTTATCAGTGAAATAAATCAGCAAATCCAAGATTCAACAGATCGCCTAGAGGTCATTGAAGAGTTGATATCTTCTCAAAATGCTGCTTTATGTTGCTGtatcttttctaatttatttgtCTATCTAATGCTCGGTTTCATTACTTCATATGAGCTGTCCAGTAATAAAGCAAACAAGTTTAGGGAAACTGTTTAA

Transcript

BRAKERKRET00000012491

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q148V7	RAB11-binding protein RELCH OS=Mus musculus OX=10090 GN=Relch PE=1 SV=1
Q6P6Y1	RAB11-binding protein RELCH homolog OS=Danio rerio OX=7955 GN=relch PE=2 SV=1
Q9P260	RAB11-binding protein RELCH OS=Homo sapiens OX=9606 GN=RELCH PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004191 (this species only) · gene tree & orthology

Pfam domain

No Pfam domain signature was recorded for BRAKERKREP00000012491.1 in Hydra viridissima.

InterPro

InterPro term	Type	Description	Source
IPR040362 all species →	Family	RAB11-binding protein RELCH	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR006594 all species →	Conserved_site	LIS1 homology motif	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32059 all species →	RAB11-BINDING PROTEIN RELCH	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0032367 all species →	Biological Process	intracellular cholesterol transport	Interproscan
GO:0055037 all species →	Cellular Component	recycling endosome	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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
K26154	RELCH; RAB11-binding protein RELCH	-	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 BRAKERKREP00000012491.1 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

10TPM > 0

7Conditions

19.4Max TPM

3.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	2	1.74	19.35
Whole	6	5	9.89	14.79
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	8.62	8.62
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	7.40	7.40
symbioic hydra M9 strain · symbioic hydra rep1	1	1	6.36	6.36
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	19.35
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	11.92
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
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	14.79
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	12.36
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	11.57
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	11.07
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	9.54
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	8.62
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	7.40
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	6.36
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.