Gene detail

Detailed information of BRAKERKREP00000024682.1 in Hydra viridissima

Genomic Location: QPEY01000549.1:195123...216658
NR annotation: XP_047138178.1, msx2-interacting protein [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000024682

atgGTTAGAGAATCGCGACATCTCTGGGTGGGCAATCTACCAGAGACAGTTCGCGAAGAACAAATTCAAGACTATTTTTCAAGATATGGGCGAGTAGAGAAAGTAAAGCTTCTGGCTAAGACTAGTCCTGATGGTGGTCGAGCTGCCTTTGTAGATTTTGTGGACATTCGTTCGGCAACAAAAGCCAACGAAGCCCAAAATCGCATGGGTGAAAGGGAGTTAAGAACTAATTACAACGAACCTGGTGCTAAAAACTTAGTGGATTTCAGAGGTCATGCAATGCATAGAATACATGGAGCATACCCACCTGGaattGGCAGCCAACCTGTTGTAATTTATGCAGCACCACCAGGAGATCATTTGATTCATTCGCAAGCTTATCGCCCATTATACCACAGAGAAGAAAGAAGAATAGTGTCAGCATATACACCtttaaaaagagataaaagTCCTggTCGAAGTAGTCTCTCAGACGGCAGCCCTAGTGACAAGCGTTCTCGTGAATATTCAAGTGATTCTGATGATACAGATGATAATTCTGTGCGATCAACTTCTGTCATTATCAAAAACCTGCCTAGAAATACTGATTCAGCATTAGAAGAAGGTATCTATCATGAGTTTCGCAAAGCTGGTGAAAtagcaaaaatcaaaatcaaggGAACAGGAGCTGATCGATATGCTATAGTAAAGTTTACTAAGCCAGAAGAAGCAGAAAGAGCTACTCATAACACTGGAAAAGTTTTTCAAGGACAAACTATACGTGTATTAATTCGAGGCAATAAGAAATCTCGTAATCGCTCTCCTGAAAAAGATGATCTTGCATTTGATCCACATGCTACCAGAACTGTTTTTGTGggtaatattgaaaaaactatgATGCATGGTGAGctaagaaatatatttgagAGATTTGGTGACGTtgttGATGTAGAtataaagaaaatgcaaaCAGGATTGACAACTTATGCATTTGTGCAGTATATTGATATTAATGGAGCCATGTTTGCAAAGCGTAAAATGGATCGAGAATATATTGGACACACTATTGTGAAGATAGGATATGGTCGTGGAACACCGACAAATTGTTTGTGGATTGGCAATCTACCTTCAAATGTTGTTGATCATCAACTTTCCAAGATATTTCATCCATTTGGTTATGTTCAACACTGCTTGATTGATAAACGGTTTTGGCAAGCTCTTATTCGTTTTGAAACAATTGAAGCTTGTACACATGCTTTTGCTGAAATGCATGGCAAACATTTTCAGGGAAAGCGTCTTGCTgttgaTTACGCAAGCCCTGCTTGTCGCGACGGATTTTATCGACGCATGGAAGAGGATGGTCAACTAGATCGACGTCAATTAGAGCCTTCCCCTACTCCTCCTGATGCTCAcattaactttcaaaatgttgcTAGGGGAGGAGCATTTCAACCTCGTGGAAAcaactttattgttaaatctTATATATCAAGTGAACCAAGGGCATATGCTGAATACCACCCTGAACTTAGTTATGACAAAGGAGAAAGAGATATGTATGGAAGAGATAAAGAAAGGCCACGGGTTTATTCTCCCATGTCTCATGGAAGTAACTCTCCTAAGCATCTATATTCCCCTAAGCATACTTTATCACGTGAATCTATAAGTCCTGTTAGCAGTTTAGGATTTTATGACCGTAAGTATCGGCTTGAggagaaaaagagaaaacacAGCCATTTAGGCTCTCCTTTTCAAGaagaagttgttaaaaaaaaggagaagcgaaaaaaaaaggaaaaaaaggaGAAACAAGTTATGAAAGAAATAGAACTAGGCTACCCTCCAGTGGATATAAATTCTCCCcctttaaaattgtcaaaggaagctaaaagagaaaagaaagaaaggaagaaaaaagacaaagcaaaaagaaaatcagaaaaaaaacaaaaaaaaatcctaaagtTACGAAGTCTTCAAGAAAAACTTAGTGAAACAATTGTTGCTGAAAATCCTGATGATATATTATCAGGAGCCATGAAATCTGAACATGATACTGTTACAAGTGATCAGTTGCCTAACAAAGATGTTGAGTTGATGAAATTAAATGAAGCTAAAACAGAGAATCATGTGATTTCAGCTACACAGGTTAACAGCAATTATGAGCAATTAGACGGAAATAATATTCCTGCTATTAGTAAGGGGGAAAACCATCCCACTGAAAAAGATCAAAATGATTGTAAAACTGAATCATACATTGAGAACCAAGTTGTTGAGGAAATAAGAAAACCAGTTGCATCACCAGAAGAAGGAGAATTAAATGAAGAGGATGGAAAATCTAGTTGCAACCAATTTGCTGGCTCCCCTATTTCTCAAGATGATACCAATAAGATTTTGAGGCATACCATTAGTTTACAGCCTGTAGAGAAAACTCTATCAAGTGGCCAAATCTCTAATACAATAAAAGTAGATACACGAAGGTCTACTTTTAATTATGATTCTACAGATTCAAGTGACTGCACTTCATCAGAAAGTGATTCTTCAGATACAAGTTCAGATGactcagaaaataaaaagcatctTTATAAACGTCATTCGTGTCACCGTGAAAACCGCAAGAATTTAGAGAAGTCGAGAGAGCCAAAAGCCTACAGACAAAGTAATCGAGATGATTTTGAAAGACGTGAACATCGTGCTGAGCGTGATAGAGAAAGAGAACACCATAGATCAAGATATTTGAGTTCTGATTCTGGTCGTAGAAGTCctggtaaaaaaatgaaaagcaagTCTCCTAACAGTAATTCACCTAGCAGCTATCTGAAGCGTGATAACTCATATGATAGGCGGCATATTCGTAGCCCTTATAGTAAATCTCCAAATCATTCATTTGAACGAAAAGATCAGTATGATTTACGTGCTAGAAGAACTCATACACCACCACCACCTCCTCCGCTTACtgataaagtaaaacattCTACATCGAATGTAAGTAATGGACAAAATGCCTACCAAAGAGGATGTTCATTACCATCTAATAACAGTACAGCATCCTCACAGAGTGCTGACACATTGATGGATTTACTAAGACGGTATCCAGTGATGTGGCAAGGCCTtcttggtttaaaaaatgatacagCTGCCGtacaaatgcattttttatcaggTAATGTTCGCCTTGCAGAATCATCTCTACCACGAGCTGCTCAACCCAATGAAGTTCCTCCAACATTAAGGATATCTCAACGAATGAAGCTGGAAACATCACAGTTAGAGGGCGTTGACAAACGAATACAGCTAACAAAAGAGCATTGCATGTTGCTAGCATTGCCTTGTGGTCGCGATCCACTTGATGTTCATGCACAAACCAGAGCATTAAAAACTGGttttataacatatttacaacaaaaacaagCTGCTGGAATAATTAATACTGTAATGCAAGCTAAACAGACAACTTTTGTCATCCACATTTTTCCTCCTTGCGACTTTGCCCAAGGTCATTTAGCTCGTGTTGCACCAGATCTCCTTAACAGTGCAGCCGATAGTGGCCATTTGATGGTGCTTATTTCACCGATGTAA

Transcript

BRAKERKRET00000024682

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q96T58	Msx2-interacting protein OS=Homo sapiens OX=9606 GN=SPEN PE=1 SV=1
Q62504	Msx2-interacting protein OS=Mus musculus OX=10090 GN=Spen PE=1 SV=2
Q8SX83	Protein split ends OS=Drosophila melanogaster OX=7227 GN=spen PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002696 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07744 all species →	SPOC	SPOC domain	Domain	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012921 all species →	Domain	Spen paralogue and orthologue SPOC, C-terminal	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR016194 all species →	Homologous_superfamily	SPOC-like, C-terminal domain superfamily	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR010912 all species →	Domain	Spen paralogue/orthologue C-terminal, metazoa	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23189 all species →	RNA RECOGNITION MOTIF-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid 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

No KEGG orthology assignment for BRAKERKREP00000024682.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000024682.1 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

7.6Max TPM

1.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	1	0.30	5.46
Whole	6	5	4.80	7.56
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	2.00	2.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	2.35	2.35
symbioic hydra M9 strain · symbioic hydra rep1	1	1	1.12	1.12
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	5.46
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
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	7.56
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	6.15
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	5.53
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	5.44
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	4.11
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	2.00
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	2.35
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	1.12
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.