Gene detail

Detailed information of BRAKERKREP00000014693.1 in Hydra viridissima

Genomic Location: QPEY01000084.1:876115...876426
NR annotation: CAB4028466.1, U6 snRNA-associated Sm LSm2 [Paramuricea clavata]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9Y333	U6 snRNA-associated Sm-like protein LSm2 OS=Homo sapiens OX=9606 GN=LSM2 PE=1 SV=1
O35900	U6 snRNA-associated Sm-like protein LSm2 OS=Mus musculus OX=10090 GN=Lsm2 PE=1 SV=1
Q54TF6	Probable U6 snRNA-associated Sm-like protein LSm2 OS=Dictyostelium discoideum OX=44689 GN=lsm2 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009651 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01423 all species →	LSM	LSM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR016654 all species →	Family	U6 snRNA-associated Sm-like protein LSm2	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13829 all species →	SNRNP CORE PROTEIN FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005688 all species →	Cellular Component	U6 snRNP	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	Interproscan
GO:1990726 all species →	Cellular Component	Lsm1-7-Pat1 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
K12621	LSM2; U6 snRNA-associated Sm-like protein LSm2	-	Spliceosome	ko03041	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000014693.1 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

1TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Max TPM
whole body	18	0	0.00
Whole	6	1	0.01
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00
unannotated	1	0	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	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
SRR21134064	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
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	0.01
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058806	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	0.00
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.00
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.00
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.