Gene detail

Detailed information of FUN_006749-T1 in Siderastrea siderea

Genomic Location: contig_5:4162975...4187843
NR annotation: no NCBI-NR hit recorded
Species Siderastrea siderea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_006749-T1

ATGGACAAAACTTCTCTTTTCCAGAGCATCGGATTAAGTGAACAGAAAGCGCAAGAGACATTGAAAAATGAGGCGCTTTCCACTCGACTCGAGGCCATTATAAATGTGgcaaaagaaaaatgtgcTGGTGATATTGAGAAGCCAACCGGTGTGTTGTTGTACTCGTTGGCTAGCAGCAGTGTAAAGGAGGATTGGCAGTTCAAGTTTGTCACTGAATATATTGCAAACAAGAAACTGGCTTCATCAATACAACTGACAGCTGCCGTAGATTATATGAAGGCCAATCCTGTTTTACCTGTTAATGTGGCATCCTTTGAAGAAAACTGTGGTATTGGAGTAAATATCACGCCGGAGCAAATTGAAGATTGTGTTgaagtaataattaaaaagCACAAGGAAGAGCTTTTAAAGAAGCGGTATAAGTTTAATGTTGGAATGATAATGGGGAAGGCAAGAGAGAAGTTGAAGTGGGCAGATGGAAAGGCTATCAAAGCAGAAATTGATATGCAGATTTTAGATTTGCTGGGACCAAAAACTGAAGCGGACATGCAGAAACCAAAGACAAAGGAATCCAAGCCCAATAAAGAAGGAAAGTCAGCAAATAACTCTTCCTCAGCTGCTGAAGTGATGCAAGTAAATGGTGATGCTGGAGGTGATGAGAACAACTCACTTTTTGGAGAGGCAAGCAAATTTCACAAACCAgGGGAAAACTATACAACTCCAGGTTATGTGATTACTCCAAATACAATGAGACTAATGAAGGAGCACTTAGAAAGAACTGGAGGAAGGGTCCAAACAAGATTTCCACCAGAACCTAATGGCATTCTTCATATTGGTCATGCCAAAGCCATCAACTTCAACTTTGGATATGCCAGGGCACATAATGGTGTGTGTTACCTGAGGTATGATGATACAAACCCTGAGAAAGAAGAGGAGAAGTTTTTCACAGGAATCTTAGACATGGTTAAATGGCTAGGTTTTGAACCTTGGAAAATCACCCATGCATCTGATAATTTTGGAAAATTGTATGAGTTTGCAGTAGAACTTATTAAAAGGGGACAGGCATATGTCTGCCATCAGGAATATGAGGAAATAAAAGGCTTCAACCCACCTCCCAGCCCTTGGCGTGACAGACCCATAGAGGAGTCACTTAGGCTGTTTGAGGACATGAGGAAAGGAAAAATAGATGAGGGAAAGGCAACCTTAAGAATGAAGACCACATTGGAAGATGGTAAAGTGGACCCTGTTGCATATCGCATTAAGTTCACTCCTCATCACAGAAGTGGAGATGAATGgTGCATTTATCCAACATACGACTTCACTCACTGCCTCTGCGACTCAGTAGAAGATATTTCCCATTCCCTGTGCACAAAGGAATTTCAGTCAAGGCGTTCATCGTACTACTGGCTGTGCAATGCTCTTGACATTTACTGTCCTGTTCAGTGGGAATATGGCAGATTAAACTTGAGTTACACTGTTGTCTCCAAGAGAAAGATCGCCAAGTTAATAGCTGAAGGAATTGTCAGAGATTGGGATGATCCAAGGTTGTTTACTTTGACAGCATTGAGAAGAAGAGGCTTTCCTCCTGAAGCTATTAATAAATTCTGCAGCAAGGTTGGTGTGACAATGGCTCAGACAGTCTCAGATCCATTGCTCTTAGAGTCCTGTGTGCGAGATGAGCTGAATGTCACAGCCTCAAGGGTGATGGCTGTGCTGGAACCACTCAAGGTTACAATTCAGAACTTTGATAAGaaagtgAAGCTTGATGTACCTAATTTTCCTCAAGATCCCAGCAAAGGAAACCATGAAATTTCTTTTGGGAAAACAATCTACATTGAACAGTCAGACTTCAAAGAGGTGTCAGAAAAAGGGTTCCGGCGCCTGACTCCTGATCAGTCTGTGGGTCTGAAGTATGCTGGTATGGTGATTACACTTCATAAAATTGTTAAGGATTCCAGTGGTAAAGTGACAGAGTTGCTTGTGAATTGCGAGTCAACAGAAACTGCACAGAAACCCAAAGCTTTCGTTCACTGGGTGTCTTCCCCACTGAAGTGTGAAGTCAGGCTTTATGAGCGACTGTTTAACCATAAGAATCCAGAAGACCCATCTGAAGTACCTGGTGGTTTCATAACAGATTGTAATAAGGATTCCCTGACAGTAATCTCTGATGCACTTGTGGAACAGACAGTTAGAGAAGCTGCTGTTTATGACAAATTTCAGTTTGAGCGCATTGGTTTCTTTAGTGTTGATCCTGACAGCAGTAAACAGAAGCTGGTGTTTAATCGCACAATCTCTCTGAAGGAAGATCCCGGCAAGTCGTGA

Transcript

FUN_006749-T1

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00749 all species →	tRNA-synt_1c	tRNA synthetases class I (E and Q), catalytic domain	Domain	Interproscan
PF20974 all species →	tRNA-synt_1c_C2	tRNA synthetases class I (E and Q), anti-codon binding domain	Domain	Interproscan
PF03950 all species →	tRNA-synt_1c_C	tRNA synthetases class I (E and Q), anti-codon binding domain	Domain	Interproscan
PF04558 all species →	tRNA_synt_1c_R1	Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1	Family	Interproscan
PF04557 all species →	tRNA_synt_1c_R2	Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020058 all species →	Domain	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain	Interproscan
IPR049437 all species →	Domain	tRNA synthetases class I (E and Q), anti-codon binding domain	Interproscan
IPR050132 all species →	Family	Glutamine/Glutamate--tRNA Ligase	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR001412 all species →	Conserved_site	Aminoacyl-tRNA synthetase, class I, conserved site	Interproscan
IPR020059 all species →	Domain	Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain	Interproscan
IPR011035 all species →	Homologous_superfamily	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamily	Interproscan
IPR020056 all species →	Homologous_superfamily	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminal	Interproscan
IPR000924 all species →	Family	Glutamyl/glutaminyl-tRNA synthetase	Interproscan
IPR007639 all species →	Domain	Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal	Interproscan
IPR007638 all species →	Domain	Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2	Interproscan
IPR004514 all species →	Family	Glutamine-tRNA synthetase	Interproscan
IPR042558 all species →	Homologous_superfamily	Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1	Interproscan
IPR042559 all species →	Homologous_superfamily	Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43097 all species →	GLUTAMINE-TRNA LIGASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004812 all species →	Molecular Function	aminoacyl-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0043039 all species →	Biological Process	tRNA aminoacylation	Interproscan
GO:0004819 all species →	Molecular Function	glutamine-tRNA ligase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006425 all species →	Biological Process	glutaminyl-tRNA aminoacylation	Interproscan
GO:0017101 all species →	Cellular Component	aminoacyl-tRNA synthetase multienzyme complex	Interproscan
GO:0000166 all species →	Molecular Function	nucleotide binding	Interproscan
GO:0006418 all species →	Biological Process	tRNA aminoacylation for protein translation	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006412 all species →	Biological Process	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
K01886	QARS, glnS; glutaminyl-tRNA synthetase	EC:6.1.1.18	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 FUN_006749-T1 across 85 RNA-seq samples of Siderastrea siderea. 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.

85Samples

27TPM > 0

7Conditions

121.0Max TPM

16.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	6	15.75	120.96
holobiont · low.pH Control.temp	20	2	6.94	73.55
holobiont · control.pH_high.temp	20	8	23.32	92.66
holobiont · control.pH Control.temp	19	5	15.18	97.33
Whole organism	4	4	24.10	34.98
unannotated	1	1	34.83	34.83
live coral tissue/skeleton	1	1	48.37	48.37

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	120.96
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	56.80
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	48.06
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	39.30
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	35.85
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	14.07
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214416	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	73.55
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	65.25
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	92.66
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	77.62
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	76.94
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	58.20
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	46.09
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	41.80
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	37.14
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	35.97
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	97.33
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	52.14
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	51.78
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	48.35
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	38.83
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214470	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	34.98
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	21.91
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	20.90
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	18.61
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	34.83
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	48.37

Source: CnidoSite RNA-seq expression matrices (SSIDE_TPM, StringTie quantification over 85 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.