Gene detail

Detailed information of asel_s0001.g289.t1 in Acropora selago

Genomic Location: sc0000001_pilon:3192159...3194172
NR annotation: XP_015752092.1, PREDICTED: U6 snRNA-associated Sm-like protein LSm1 isoform X2 [Acropora digitifera]
Species Acropora selago · 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
Q8VC85	U6 snRNA-associated Sm-like protein LSm1 OS=Mus musculus OX=10090 GN=Lsm1 PE=1 SV=1
Q5E9Z8	U6 snRNA-associated Sm-like protein LSm1 OS=Bos taurus OX=9913 GN=LSM1 PE=2 SV=1
O15116	U6 snRNA-associated Sm-like protein LSm1 OS=Homo sapiens OX=9606 GN=LSM1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002587 (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
IPR044642 all species →	Family	U6 snRNA-associated Sm-like protein Lsm1/8	Interproscan
IPR034104 all species →	Domain	Sm-like protein Lsm1	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15588 all species →	LSM1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000290 all species →	Biological Process	deadenylation-dependent decapping of nuclear-transcribed mRNA	Interproscan
GO:0000339 all species →	Molecular Function	RNA cap binding	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0016070 all species →	Biological Process	RNA metabolic process	Interproscan
GO:1990726 all species →	Cellular Component	Lsm1-7-Pat1 complex	Interproscan
GO:0000956 all species →	Biological Process	nuclear-transcribed mRNA catabolic process	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
K12620	LSM1; U6 snRNA-associated Sm-like protein LSm1	-	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0001.g289.t1 across 24 RNA-seq samples of Acropora selago. 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.

24Samples

24TPM > 0

1Conditions

241.6Max TPM

112.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
coral larvae	24	24	112.95	241.64

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR14308005	coral larvae	coral larvae	not recorded	not recorded	SRP315987	241.64
SRR14308022	coral larvae	coral larvae	not recorded	not recorded	SRP315987	131.25
SRR14308019	coral larvae	coral larvae	not recorded	not recorded	SRP315987	125.29
SRR14308006	coral larvae	coral larvae	not recorded	not recorded	SRP315987	118.83
SRR14308008	coral larvae	coral larvae	not recorded	not recorded	SRP315987	118.76
SRR14308027	coral larvae	coral larvae	not recorded	not recorded	SRP315987	118.19
SRR14308024	coral larvae	coral larvae	not recorded	not recorded	SRP315987	116.90
SRR14308026	coral larvae	coral larvae	not recorded	not recorded	SRP315987	112.84
SRR14308018	coral larvae	coral larvae	not recorded	not recorded	SRP315987	112.51
SRR14308012	coral larvae	coral larvae	not recorded	not recorded	SRP315987	110.47
SRR14308015	coral larvae	coral larvae	not recorded	not recorded	SRP315987	110.43
SRR14308004	coral larvae	coral larvae	not recorded	not recorded	SRP315987	109.04
SRR14308023	coral larvae	coral larvae	not recorded	not recorded	SRP315987	105.90
SRR14308007	coral larvae	coral larvae	not recorded	not recorded	SRP315987	103.17
SRR14308016	coral larvae	coral larvae	not recorded	not recorded	SRP315987	102.97
SRR14308021	coral larvae	coral larvae	not recorded	not recorded	SRP315987	102.49
SRR14308017	coral larvae	coral larvae	not recorded	not recorded	SRP315987	102.42
SRR14308014	coral larvae	coral larvae	not recorded	not recorded	SRP315987	101.65
SRR14308013	coral larvae	coral larvae	not recorded	not recorded	SRP315987	100.54
SRR14308025	coral larvae	coral larvae	not recorded	not recorded	SRP315987	100.50
SRR14308010	coral larvae	coral larvae	not recorded	not recorded	SRP315987	99.68
SRR14308020	coral larvae	coral larvae	not recorded	not recorded	SRP315987	96.95
SRR14308011	coral larvae	coral larvae	not recorded	not recorded	SRP315987	96.75
SRR14308009	coral larvae	coral larvae	not recorded	not recorded	SRP315987	71.52

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 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.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora selago tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	18	asel_s0244.g53.t1	0.966581918396203
Negatively correlated	8	asel_s0082.g30.t1	-0.912399807366688

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora selago, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

DNA methylation (bisulphite samples)

Sample	Methylation profile
Coral_Fragment_Parent	open
Larval_Pool_Offspring	open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →