Gene detail

Detailed information of g4199.t1 in Montipora capitata

Genomic Location: Sc0000076:681998...685837
NR annotation: XP_015760582.1, PREDICTED: U6 snRNA-associated Sm-like protein LSm3 [Acropora digitifera]
Species Montipora capitata · 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
Q32PE9	U6 snRNA-associated Sm-like protein LSm3 OS=Bos taurus OX=9913 GN=LSM3 PE=3 SV=3
P62310	U6 snRNA-associated Sm-like protein LSm3 OS=Homo sapiens OX=9606 GN=LSM3 PE=1 SV=2
P62311	U6 snRNA-associated Sm-like protein LSm3 OS=Mus musculus OX=10090 GN=Lsm3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009089 (this species only)

Pfam domain

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

InterPro

InterPro term	Type	Description	Source
IPR040002 all species →	Family	U6 snRNA-associated Sm-like protein Lsm3	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR034105 all species →	Domain	Sm-like protein Lsm3	Interproscan
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13110 all species →	U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM3	Interproscan

Gene Ontology

GO term	Category	Description	Source
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:0033962 all species →	Biological Process	P-body assembly	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
K12622	LSM3; U6 snRNA-associated Sm-like protein LSm3	-	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 g4199.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

48TPM > 0

3Conditions

114.1Max TPM

60.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	64.30	114.15
whole organisms · low pH treatment	15	15	59.22	92.22
whole organisms · extra low pH treatment pH treatment	12	12	55.04	97.39

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	114.15
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	111.37
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	108.56
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	97.48
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	86.35
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	84.37
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	72.31
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	71.68
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	70.11
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	68.25
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	64.67
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	64.33
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	63.30
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	58.72
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	55.41
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	37.95
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	36.42
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	31.47
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	20.91
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	17.34
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	15.23
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	92.22
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	88.36
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	81.14
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	80.17
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	77.60
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	72.91
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	70.39
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	69.71
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	66.04
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	61.99
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	50.55
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	28.43
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	19.50
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	15.29
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	14.04
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	97.39
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	87.24
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	82.83
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	82.29
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	77.72
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	67.82
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	65.70
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	38.55
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	38.16
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	11.17
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	6.29
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	5.33

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.