Gene detail

Detailed information of gfas1.m1.1422.m1 in Galaxea fascicularis

Genomic Location: Sc0000040:280433...289566
NR annotation: XP_015773621.1, PREDICTED: serine--tRNA ligase, cytoplasmic-like [Acropora digitifera]
Species Galaxea fascicularis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

gfas1.m1.1422.m1

CCCGTTCGTCCGAGGTATGTGGGTCGCCCTCTTTGGATTGCATCAGCAGAAGTTCTTTCCAGTAATCTTTAGGTATCCAAGGTACTTCTCGATCTCCTTTATCAGAATGGTGCTGGATTTAGACTTGTTTAGGACTGACAAAGGGGGTGATCCCGAAAAGATCCGCGAAAATCAGAGCAAACGGTACAAAGACACGAAGCTTGTGGACGAAATTGTCGCGGCGGACACCAAATGGAGAAAATTACGGTTCTCGGCGGATAACTGGAACAAACTGAAGAATTTATGCAGCAAACAGATCGGCGAAAAGATGAAGCGCAAAGAACCTGTTGGTGACAGTGAAGATTTGCCTGAAAATGTAGTCAGTGGTTTGGAGGAACTTACCCCTGAAATGTTACAGGGTCTCACCGTGACTCAGATAAAAAGTATAAGGACACTCATTGATGGAAATATTGCCAAGTGTAATGAAGAGGTCATCAGTGTGGAGCAACTGCGTAATGAGAAACTGTTTGAAGTTGGAAATTTTTTACATGAATCAGTTCCCATCAGTAATGATGAGGAAGAAAACAAGGTGATGAGAACCTGGGGGGACAGTTCAGTAAAGAAGAAGTATTCCCATGTAGATCTGGCGTATATGGTTGATGGAGTTGATACCGAACGGGGTTCCCTTGTGGCTGGCAGCAGAGGCTACTTTCTCAAGGGCCCACTTGTTTTCCTGCAACAGGCCCTTGTCCAGCTTGCAACACGCATGCTGTACAAGAAGGGCTTTGTTCCTTTGTACACGCCCTTTTTCATGACAAAGGAAGCAATGCAAAAAGTGGCTCAACTAAGTCAGTTTGATGAGGAGCTGTACAAGGTAATTGGAAAAGGTGCTGATGAGGCTGGCTATGAAGAAAGATATTTGATTGCAACCAGTGAACAGCCAATTGCAGCACTCCACCGAGATGAATGGATGGCTGCAACTGCTGATGAACTTCCAAAGAAATATGCTGGATTCTCTTCATGTTTTAGACAAGAGGCAGGTTCCCATGGCAGGGACACACGTGGTATTTTCAGAGTACATCAGTTTGAGAAGGTGGAGCAGTTTGTTATCTGCTCTCCTCTTGATGACATTTCATGGCAAATGTTTGATGAGATGATCGGCAATGCAGAGGAATTCAATCAGGCCCTGGGAATCCCTTACAGGATTGTTAATATTGTGTCTGGTGAACTCAATAATGCAGCAGCAATGAAGTATGATTTGGAAGCTTGGTTTCCTGGCAGTGGTGCATTCCGTGAGCTGGTGTCCTGCTCAAATTGCACTGATTACCAGGCAAGAAGATTGCAAGTTCGGTTTGGACAGACCAAGAAAATGGGAGAACAGACGAAGTTTGTTCACATGTTGAACGCCACAATGTGCGCTATCTCGAGAACGATTTGCGCGCTGTTGGAGAATTACCAAACAGAAGAGGGAATTGCGCTCCCTTCTGTACTCAAACCATTCATGCCAGAGGGATTGGATTTCCTGAAATTTGTTAAACCGGCACCAATTGACGAGCAGCCAGAGGCCAAGAAGCAGAAGAAGAAAGTAAAGAACAAACCAGCTGCCCAGCCCGAGGGCTGCCTAGAGGCGAAAATGGAAAATATGGATGTTAGCAAAGAATGAATCTTCGTCAATTACTATATCAGTTATATCAGTCGGCAGTCTTACGGTGTCTTCACGCCGTCCAATAACTTATTTAGACTAGGGTTATCGTTGTCGCCTGATCAAGGTTGAATAACGTGTAGCATAACACGCAATAAAATCTTATTTTCTCTTTTTGGAGGAAAGAGGAAACGTTACCAGCATGGAATCGACTCAATGGAAACAAAATGTGCGCTTATCGCCTCTTGATTTGTTAATCAAAACCATCTTGCTTCCTTGCCCCTTCCCTCGCCTTCATCGCAGACGAGATTGTTTTGTTTGAGCTTTTTATCACTCCATGAATTCACCGATGGTTTCGTAGATTACGTTTTATGGCAGAAAGCAGCGTATTATATCCAATGTCACAAACCCATTGAACGCTGTAGTACTGATTTTACATCCTACTCGCGATCATGAGAAGAGAAAGGACAAGAACGAAGAAAAGCACTGTGTACTGTTAAAAGCAAGCATATTTTTTCGTTGAATGAAACCTTGGCTACTTTTCCTGGGCGTTACAAGGGTTTCAGATATTCCCCTCGCTGAAAACTAATTTTAAAAAAATGTCGAGTATTTCCACGAAGACATTTGAGGAGTAGAATACAAAAATTGGGTTTCATTTGTCAACTGAGTTGATAAAGAAAACAAGAGTAATGTAAATAAGAATAAAACGCTACCGTCTGTTCAGCTAGCCTACTGATGCTGTTTATCCTTTCCCATAAAAATGAAATTATCGGTTGGAATTCTCAATTGACTAAAAACCGTCATTTTCAACAACGAATGGTAACTTCTACAAATTATTTGCCCTGTCAGTCAAGGTTTTTTTGGTGTTGCTCGCTTAGTTTTGACAAAAATACAATAAGATCGTAGTACAATGTACCTGAACTTTCACAACGCAGTGACGCTTAGTGAATCATCTAAAAGTGGATAAAACGTAAGGGGAAGAGAATGTGGCGGCGACGTGACTTCTCCAGTCGCCGCTTCTCGTGGTCTGGAGTGGGACAAACATTTAAGATTAGGAACGTGGTAAAGGGGATCTTCGTGCAGTTAGCCATGCAAGGTTAGTGATGGAATCCAGACAACATTTTCCATGTTTGCAAAAAAAGAAAAAAGTTGATTAACGTGTGACAGCATTAGCGAGACCCTGAACGGAAATTAAAGAAACTGTTTTGTGATTAGGACTTAAGGAAATATTCCAAATTTAAGACAACACAAATTTTTGTTATACTCCATGTATTCTGAGAGACTGATTTAGCTCCCAGGCATGATGATGATGATGGGAGCCTGTTTTGATTACTATCGGTCTCTAAACATCAATATCCTGACTTTATCAAACATATTGACTGATGTATTTACCCCATTTAAAATCAGTACACCCTGTTAGCAAAATAAAAGAATCGCTGAACGGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5R9K9	Serine--tRNA ligase, cytoplasmic OS=Pongo abelii OX=9601 GN=SARS1 PE=2 SV=3
P26636	Serine--tRNA ligase, cytoplasmic OS=Cricetulus griseus OX=10029 GN=SARS1 PE=2 SV=2
P49591	Serine--tRNA ligase, cytoplasmic OS=Homo sapiens OX=9606 GN=SARS1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003390 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02403 all species →	Seryl_tRNA_N	Seryl-tRNA synthetase N-terminal domain	Domain	Interproscan
PF00587 all species →	tRNA-synt_2b	tRNA synthetase class II core domain (G, H, P, S and T)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006195 all species →	Domain	Aminoacyl-tRNA synthetase, class II	Interproscan
IPR002317 all species →	Family	Serine-tRNA ligase, type1	Interproscan
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR015866 all species →	Domain	Serine-tRNA synthetase, type1, N-terminal	Interproscan
IPR033729 all species →	Domain	Serine-tRNA ligase catalytic core domain	Interproscan
IPR002314 all species →	Domain	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Interproscan
IPR042103 all species →	Homologous_superfamily	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Interproscan
IPR010978 all species →	Homologous_superfamily	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11778 all species →	SERYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004828 all species →	Molecular Function	serine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006434 all species →	Biological Process	seryl-tRNA aminoacylation	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	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
K01875	SARS, serS; seryl-tRNA synthetase	EC:6.1.1.11	Transfer RNA biogenesis	ko03016	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of gfas1.m1.1422.m1 across 22 RNA-seq samples of Galaxea fascicularis. 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.

22Samples

20TPM > 0

4Conditions

206.7Max TPM

103.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
coral holosome · Control	7	7	121.01	206.65
coral holosome · 30ic treatment	6	5	93.18	170.05
coral holosome · Prometryn (herbicidess) treatment	5	4	84.51	120.39
coral holosome · Prometryn (herbicidess) and 30ic treatment	4	4	113.63	152.75

Per sample · hover a bar for the full sample record

Show the sample table (22 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR27118485	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	206.65
SRR27118491	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	139.52
SRR27118492	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	109.58
SRR27118480	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	105.61
SRR27118488	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	102.19
SRR27118486	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	91.95
SRR27118487	coral holosome · Control	coral holosome	not recorded	Control	SRP476288	91.55
SRR27118477	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	170.05
SRR27118476	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	102.90
SRR27118466	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	102.61
SRR27118478	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	95.30
SRR27118479	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	88.23
SRR27118468	coral holosome · 30ic treatment	coral holosome	not recorded	30ic treatment	SRP476288	0.00
SRR27118484	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	120.39
SRR27118482	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	106.76
SRR27118469	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	103.46
SRR27118481	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	91.94
SRR27118483	coral holosome · Prometryn (herbicidess) treatment	coral holosome	not recorded	Prometryn (herbicidess) treatment	SRP476288	0.00
SRR27118489	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	152.75
SRR27118490	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	106.84
SRR27118472	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	98.74
SRR27118475	coral holosome · Prometryn (herbicidess) and 30ic treatment	coral holosome	not recorded	Prometryn (herbicidess) and 30ic treatment	SRP476288	96.20

Source: CnidoSite RNA-seq expression matrices (GFASC_TPM, StringTie quantification over 22 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 Galaxea fascicularis 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	33	gfas1.m1.5390.m1	0.899775791875334
Negatively correlated	67	gfas1.m1.4642.m1	-0.898740611350074

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 Galaxea fascicularis, 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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

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 →