Gene detail

Detailed information of alor_g12673.t1 in Acropora loripes

Genomic Location: Acropora_loripes_71:711537...741399
NR annotation: XP_044176190.1, LOW QUALITY PROTEIN: uncharacterized protein LOC114950879 [Acropora millepora]
Species Acropora loripes · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

alor_g12673.t1

ATGAGCGGAATATCAGAAATGGCTGCATTTAGTCAAAGTGACATTAGGGTTTTTAAACAGCTGCAAGATGATGACCTCACAGAGCTGGACAAGATTTATCTCATTCTTGCAGAAAACAGCCTCCCAGACTCATTCAATGTTCTTTGCTATGATCTGGGAATTAAAACATTTGAAGACTGGCGTAGACTTGATGATGAGAACTTAGAGAGATTTAAACTTTTACCAAAGTTTGCCAAGGCACAACTGAAGCTTCTTCCATTCAAAGCAGAAAATACTGATTTTGTTAATTTAGCACTGAAACATGGAAAACGACCTTACAAAGATCAACTGCATTCTCATGGAGTCCCATTCATACCTGTCAGTGAAATTCAAGTTTTAAAAAGGACATCATATGGTCCCATTTCAGGATCTGTTTTTGAAGCCATCTGGAATAAACCCAGTGGAGAACGGGTCAACGTTTGTTTGAGGTACGATAGATCTCTTTCTCAGAGGAAAGACTTCATTCATGAAGCTGAGATGGCAGCATTTTTAAACCATGAGAACATTCTTCGCCTTCATGGTGTTGTTTTACCAGGACTTTACATCGATTCTGTGGCATTGGTGGTAGATTATGCTGAATATGGGAATCTTCATGAATCCATGCCAAATCAATCTGTTGCCAGCTTGGTTCAAACTGTCACACAGCTTGCCTCTGCTCTGGAATACCTTGAAAATAAAAATATGAAACATCGTGGACTTTCTTGGACATCCGTTTTTGTAATGAAACCTGGGAAGATCAAACTTGGAGCTTTATGGGGATGTGTCCACCAAGCTGATGGGAAAAAAAGGAATGAAGGAAAACATAGTCAATCAGGGGAGGAGGTTGTCTGGCTTGGACAATGTGCCAAAGAGTTATTTCATGGTCTGCAATTCACTAAGAAGTATTATGCTTTCACATTACGTGAACAGCTTGCAAACAATGTCTTTTGTCCTGAAGAGCTGAGGAGTCTTTTTGATCAATGCTGTGCAAGGGTCATCAATAAAAGGCCTTCATTATCTCATGTTGCCAAAACTCTTCTGGATTATTCCCTTCCTAAACTAGTTGTGACCTCAGAATTGAGAGCTGAAACTCCTAATGAACTCAGTTGCAAAGAGGGTGAAGTCATTGTCTTGATCTCTACGACTGTCCCAGGGGAATTCAGGACTAAGACTGGGTTATGGCTTGGTGAAAAAAGGTCGGGTGCTGTTGGTGTATTTGATCCCTCAAAAACAAGAAAAGTTATTGATGGTGAGGAGATTGTGTGGGATACATTGAACGTCAATGAAGAAGATGAAAAATCACCCTCAGGGTCAACACTGGCGGGGGAGGGCAACGACACGTCAGTGGATGTAGACAGGGTCATGAACTGGCAGCTTGTGAAAAATGAACAGTTTACCTCCGAGTTTGCTGATGATATAGCCAGACTAGTGGTGGGAGAACTTAAGTGGAAGGAACAAGGAGAAGAAGAAAAGTCACCCACGGAGGCGGCGGTGAATGAAGTTGACCAAAATGATAATACCCAAGTTGCAGAAACTCCTTTAGTTGAAGGACGCCAGCTTCCAATTCAGGTGGTTGCAGCATCTTCGAGCGTAGAGGAGCCAACTATTCCTCGCCCCGATGTTTTGCTCGGCCATGATCCTGACCTGATCGCAGATCCAGAGTTCGACTTAGAAATCGACACCTCTGGCGAGGTCCCAGAAGATGTGAAGGCCCTTGTCCATAAATACTTAGAGAGTCAAGAGGGTGACCAGGAGAGTAGCGACAAGGAGACTATCAAAAAGAGCCTCTCTGGGAAATCCTTCGAGCAGCACGTTCGACGACCCTTTCACCGTGTAGATAACACTCGCTCTGGAGAGGATGGTGGCATTGAGAAAGTTCGTCAAGAAATTAGAGAGGTTTTGCGTTCGGAACCCTACATGGGAGAGGATGTCCCGGTTCGCTGGTTTAACTTCGAGAAAGTTTTGGAAGCTTTGGTCAAGCAGAAGACATTTTATCTTAATGTCATCCAGCTTTATAACATAGTACGTAAGCTCATCACTATTCGGCCTTTTGATGAACAGAATCCACGTCATGCGGCAGACTGGAACGAGTTGGAACAAACTGGCCTGTTGAGCATGCGCCTGGTAGATCACGTGTTTTCTGAGTTTCTGTGCGACGGTCAATTACAGACCGATATCCTTTCCATGATGGAAACGTATGGTTTGATCGCCAAATTTACGTCAAAAAACGCTGAAACCACATCATCGCCACCTGTTAAATACTTTGTTCCAGCGCAGCTCTGTTCGTGTCCTGAGTGGAGTGGTCTTGATCAGCTTGTGTACAGTATACCCCCGCTTTACATTCACTTTCCCGATGGTTTTCTCCCGAATGGACTTTTCCCGCATCTTGTCTCTCGACTAATTTCTGTCTGCTCCGAACTCGGATGCACCGAGGAGCCGAACTTGTTCCAGAACGTTGTCAGATTCATTTTGGGAGGAAGTGATTTGCTTTTCATTTGCAAGCAGTCTTTTGTTAAGGTGATAATCGCAGAAAGAGAAGCAGATCAACGAGACAATGGACTTGCTCATAAAGTGCGCGAGTGCCTGGAGTCGATTCTTGACCGTTTGGCAAACGACTTTGCGTGTCTACGTTACATGCGTTACCAGTTCTGTGTGATGTGTCCAGCGTGTTCAGCTGCAGGCGAGGCGCGGGTTAAACACGGGGCACAATCTTGTTCTCTCAGTGACTGCATCCACTTCCTTCCGATCTGCAAAGAAGGAAATTTGATTTGCAAGAAGACGTTCGGAGCGCGGTCACATGTGGACATTCCCGGTTTGGATGAATGGCGTGGTTCTGCAAGAAAGACCAACGATCTTGATAACCCGCACTCCGCTCCAATAATGAAGGGTGAAGAGGTAAAAAAGAAAGGAATTGAGGATGGAAAGATGAATATCCATGGGGAGCCTGTGGTGCGTGCTGACGTATTTATCTCATACCAGTGGGATCATCAGGACACGGTCAAACTTCTCAAGACAAAGCTAGAGGAGGCTGGGTTCCACTGTTGGATGGATATCAGTCGCATGGGAGGGGGAGACGCCTTGTTTACCGAGATCGACGCAGGAATTAGGGCAGCAAAGGTGATCATATCTTGCGTGACGCAGCGTTTCTGTCAATCTGAAATGTGCCAACGAGAGTCAACTCTTGCTGATAGCTTAAGGAAGCCAATAATTCCCGTATTGTTGGAACTCGTCAAATGGCCCCCTCCTGGACAACTCGCTTTGATATTTGCCAAGTTGCTTTACATCGACATGTCCTTAAACCCTGGAACGTTTCCTGCGGCAAAATTACAGGAACTTTTTCAGAAAGTCAGAGGTCACGTTGAGATGGTTCTGGATTTAGACTTATTCAGGGCTGATAAAGGGGGAGACCCCGAAAAAATACGCGAAAATCAGAGCAAGCGGTACAAAGATGCAAAACTTGTCGACGAAATAGTAGAGGCGGATACCAAATGGAGAAAATTAAGGTTTTCAGCGGACAACTGGAATAAACTGAAGAACTTGTGCAGCAAACAGATCGGCGAAAAGATGAAGCGCAAAGAAGCTGTTGGAGACAGCGAGGAGCTTCCAGACAATGTGGTCAATAGTTTGGAGGAGCTTACACCAGAAATATTACAGGGACTTACTGTGACCCAAATCAAAAGCATACGGACTCTCATTGATGGAAATATTATGAAGTGTAATGAGGAAGTACTTAAAGTGGAACAAGAGCGAAATGAGAAATTGTTTGAAGTTGGAAACTTTCTTCATGAATCAGTTCCCATTAGCAATGATGAGGAGGAAAACAAAATTATGCGCACCTGGGGGGACAGTTCAGTCAGAAAGAAGTATTCCCATGTAGATTTGGCATACATGGTGGATGGAGTTGACACTGAGCGTGGTGCCCTTGTTGCTGGCAGTAGGGGCTATTTTCTCAAAGGTCCACTTGTATTCCTACAGCAGGCTCTGATTCAATTGTCAACACGCATTCTGTACAAGAAGGGTTTTATTCCGTTGTACACACCTTTCTTCATGACCAAAGAAGCAATGCAAAAAGTGGCTCAACTGAGTCAGTTTGATGAGGAACTGTACAAGGTTGTTGGCAAAGGCGCAGGTGAAGCTGGCTATGAAGAGAGGTACTTGATTGCAACTAGCGAGCAGCCTATAGCAGCTCTTCACCGAGATGAATGGATGTCTGCTTCAGCTGACGACCTTCCAAAAAAATATGCTGGATTTTCTTCGTGTTTTAGACAAGAGGCAGGATCCCATGGTCGAGATACACGGGGCATTTTCAGAGTACATCAATTTGAGAAGATTGAGCAGTTTGTGATCTGCTCCCCTCTGGATGACATCTCCTGGCAAATGTTTGATGAAATGATTGGAAATGCCGAGGAACTGAACCAGGCTCTGGGAATACCTTACAGAATTGTTAATATTGTTTCTGGTGAGTTAAATAATGCGGCAGCCATGAAGTACGATTTGGAGGCTTGGTTTCCCGGCAGTGGAGCTTTTCGTGAGTTGGTATCCTGTTCGAATTGCACAGACTACCAAGCAAGAAGATTGCAAGTTCGTTTCGGACAGACCAAGAAAATGGGAGAACAGACCAAGTTTGTTCACATGTTGAATGCCACAATGTGCGCTGTGTCGCGAACCATTTGCGCGCTGTTGGAGAACTACCAAACGGAAGAAGGGATTGCGCTTCCACAAGTACTGAAACCCTTCATGCCCGAGGGCATGGATTTTCTTAAATTTTCTAAATCGGCGCCTATAGATGAGCAACCTGAAGCCAAGAAACAGAAGAAGAAAGGAAAGAACAAGTCGGGAACGCAGACCGAGGGTTGTCTAGAGGCCAAACTCGAAAATATGGATGTCAGCAAAGATTGA

Transcript

alor_g12673.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9GMB8	Serine--tRNA ligase, cytoplasmic OS=Bos taurus OX=9913 GN=SARS1 PE=2 SV=3
P26638	Serine--tRNA ligase, cytoplasmic OS=Mus musculus OX=10090 GN=Sars1 PE=1 SV=3
P26636	Serine--tRNA ligase, cytoplasmic OS=Cricetulus griseus OX=10029 GN=SARS1 PE=2 SV=2

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
PF13676 all species →	TIR_2	TIR domain	Domain	Interproscan
PF00587 all species →	tRNA-synt_2b	tRNA synthetase class II core domain (G, H, P, S and T)	Domain	Interproscan
PF07714 all species →	PK_Tyr_Ser-Thr	Protein tyrosine and serine/threonine kinase	Domain	Interproscan
PF02403 all species →	Seryl_tRNA_N	Seryl-tRNA synthetase N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045864 all species →	Homologous_superfamily	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Interproscan
IPR000157 all species →	Domain	Toll/interleukin-1 receptor homology (TIR) domain	Interproscan
IPR042103 all species →	Homologous_superfamily	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Interproscan
IPR000719 all species →	Domain	Protein kinase domain	Interproscan
IPR001452 all species →	Domain	SH3 domain	Interproscan
IPR002314 all species →	Domain	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Interproscan
IPR001245 all species →	Domain	Serine-threonine/tyrosine-protein kinase, catalytic domain	Interproscan
IPR033729 all species →	Domain	Serine-tRNA ligase catalytic core domain	Interproscan
IPR002317 all species →	Family	Serine-tRNA ligase, type1	Interproscan
IPR010978 all species →	Homologous_superfamily	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Interproscan
IPR035897 all species →	Homologous_superfamily	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Interproscan
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan
IPR006195 all species →	Domain	Aminoacyl-tRNA synthetase, class II	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR015866 all species →	Domain	Serine-tRNA synthetase, type1, N-terminal	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0004672 all species →	Molecular Function	protein kinase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	Interproscan
GO:0000049 all species →	Molecular Function	tRNA binding	Interproscan
GO:0004828 all species →	Molecular Function	serine-tRNA ligase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006434 all species →	Biological Process	seryl-tRNA aminoacylation	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 alor_g12673.t1.

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

Co-expression network

Genes whose expression across the transcriptome samples of Acropora loripes 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora loripes, 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.	no expression matrix	–
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 →