Gene detail

Detailed information of BRAKERKREP00000015375.1 in Hydra viridissima

Genomic Location: QPEY01000092.1:807092...816872
NR annotation: XP_047145597.1, pumilio homolog 2 isoform X2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000015375

ATGCATGACCTTATTTGGCAGCAGCAAAACAAATCAGTTGTCAACAACTATCAAGGAGAGAACACACGTAATGCGCCTAATGACCATCCTCAGCAAACCCATTTCAACGATTCTTCTGGCTGCTCTGTGAAAATAACTgctgaacaaaaaaacaatttttttaaaaacaatattgcaGCTGTCAATGATTGGAGTGTAAATATTGATGATAATCAAAATCGAAAAcaaaTTTGGAATAAATCTAGAGATAAAGCAttagacttaaaaaaacctaataGTCCTCCAACCATGTTTACTTTTGATAACCACTGGCAAGAACCATCTTGGAGCTTAAGTGATACAAGCAGTGATAAATCAGAACATGCGATATCTCAGCCTATTACAATGGTTCAAAGAAGGCATGAACAATATGGAGGGCCTCAACATGTGGTAACTTCCCCTAGATCAGCTGATGGTTCTGTGCTTGGAGTTCACATGGTAGAATATGTGCTTGCTTCCTCTCCAGGAGGTCATGATTTAGAATCTCGCATGAAAGAAATGAACATTGTATCGGATGGTATTAATCAAAAAGCACATAATGGAAATCCTGTTTCTCAAACATTtgaagaagatgaagaagTTGAAGTCCATATTCAAGATGATGAGCAGTCGCTcTCTCAGCACACAAGTAATGAAAGTCATAATTCCCCATTGCCAAACCAGAAAGATTCTCTTGGTGGAATAATAGGTGGGCGATCTTCCAATGGCACTCCTATCAAATCAATATCATCACAAAATAACTCCCAGGTTACTTCACCTGTGCCGTTTAATCAATTGGATCAAAGTGAAATGAGACATATAGATTCATATGATAGTAATATGCTACATCAGTATGATATTATTGGTACAACTAATCAGCAGCATATGTCTGCTAACCCTCATTTAGTTTTTGGGTCTAACCCTCAACAACAGCAAGCAATGGGTATGCCTAGCCCTTATTATGTTGCTAGTGCTGCAGGGCAAGACCCTTATGGCCAAAGTGCTGGTATCCCATTAGTTAATGCGCAAGGACAAACAACTATGATTCATCCTCAGTATGCTGCTGCTTATGGAATCCAGTCGATTGTATATGCAAACCAAAATGGGAATGCTTACCTTCAACAACAGTCTCAAACAACTAGTGCTTCGACTAGTACAACACATCAATCATCTCAGCAGCAAATTAATGGTCAGCAGTTACCTCCAGGCTACCAAGTTGTTCAAGCCCCAATAAATTTTCCTACTGGATCTACATTCTATGATCAGCATGGTAATCCGGTTATAATTAATGGTAGAATGTTAACTAATGGTGTTAATCAAATGGGGCAAACTGTTCGAATGGTTTCTTCTATGGTTTTGAATCCAAATGCTCAGTCAACTGTTAGTCCAGGAATGCATAGTGGAAATTCATCTTCAATTCATATGTATAATCAACCAACTCAGCCTGGGCAGCAGCAGCAGAGAggaggGATCAATCTTGGATATTTATCTACTGGTCAATTAGGTCCTCTTCCAGGTCAGAATACAATGCAATTGCAAACCACAGGTCCTGTTGGTGTCATAGGTGGGCATTTACAATCTACAGGGACTGGCCCATTGCCATCACCTGGAGGTCAGCGTGATGTATACAGTACTCTTGGTGCAAAGCGCTCTGGTGGAACTCCTGTTTATACTCCAGGCATGGTTGGATCATACAACTCATTAACTGTTAATACTCCACTTGCTAATTCCCTTAACATGACTAATCCGAATACTTCCCCTTTACATTCACAGGGGCAAGCATCTTTTGAAATTGGAAGTCCTGCTAATGGAAGTAGACTATCTAACtatatgagttttttaaactctcAAGGAGATCGTAGATTCAGTTCCTCAGCTTTATCAAGTTCCTTTCTAGGATCAAGTGCCAGTTTATACAGGCGTGTTGGTGCAAGAGATAGTGGTCGATCCAAATTGTTGGAAGATTTCCGAAATAACCGCTTTCCAAATCTTCAACTTCATGATTTACAAAGGCATATTGTGGAGTTTTCCCAAGATCAACATGGTTCACGATTTATTCAGCAGAAGCTAGAGAGGGCTAGTGTTTTGGAAAAAACCATGGTTTTCAATGAAATTCTATCAGCTGCTTATAGTTTAATGACAGATGTATTTGGTAATTATGtcatacaaaagttttttgagttCGGTTCTCCTGAGCAGAAGCTTTTGCTAGCACAGAGGATTAAAGGCCATGTTCTACCTTTAGCTCTGCAAATGTATGGTTGCAGAGTTATTCAAAAGGCTCTTGAAACTATACCTTCAGAAATTCCTATTCatGGTGAATTAGTTAAAGAATTAGATGGTCATGTCTTGAAGTGTGTTAAAGATCAAAATGGGAATCACGTTGTTCAGAAGTGCATTGAGTGCATTGACTCAACTCAGCTTCAATTTATTATAGATGCATTTCAAGGACAGgTTTATTCATTGTCTACACATCCTTATGGTTGCAGAGTGATTCAAAGAATTCTTGAGCATTGTACACAGGAGCAAACAGCTCCAATATTAGCAGAGCTCCATGAGCATACAGAACGTCTTATTCAAGATCAATATGGAAACTATGTAATACAACATGTTTTAGAACATGGCAGTCCTGAAGACAAATCTACTATTGTTAATATTGTGCGTGGTAATGTTTTGCTGCTGAGTCAGCATAAGTTTGCTAGtaatgttattgaaaagtgTGTTACCCATGCATCAAGGCAGGAAAGATCTCTTCTCATTGATGAAGTCACTAATTATCCTGATGGtccTCATGGAGCATTATATATGATGATGAAAGACCAATATGCAAACTATGTTGTCCAAAAGATGATAGATATAGCTGAGCCAATTCAGCGTAAAGTACTTATGATCAAAATTCGTCCTCATGTATCTACATTACGCAAGTATACCTATGGAAAGCATATATTAGCCAAGTTGGAGAGCTTTGAAAAGGCATATATGCAGGCGCcagatcttttatttttaccagtCAATGCACCAATTACTtcatactaa

Transcript

BRAKERKRET00000015375

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8TB72	Pumilio homolog 2 OS=Homo sapiens OX=9606 GN=PUM2 PE=1 SV=2
Q80U58	Pumilio homolog 2 OS=Mus musculus OX=10090 GN=Pum2 PE=1 SV=2
Q2VB19	Pumilio homolog 1 OS=Gallus gallus OX=9031 GN=PUM1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003727 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00806 all species →	PUF	Pumilio-family RNA binding repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR001313 all species →	Repeat	Pumilio RNA-binding repeat	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR033133 all species →	Domain	Pumilio homology domain	Interproscan
IPR033712 all species →	Domain	Pumilio, RNA binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12537 all species →	RNA BINDING PROTEIN PUMILIO-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0003730 all species →	Molecular Function	mRNA 3'-UTR binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0010608 all species →	Biological Process	post-transcriptional regulation of gene expression	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
K17943	PUM; pumilio RNA-binding family	-	Spinocerebellar ataxia	ko05017	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000015375.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.