Gene detail

Detailed information of g17229.t1 in Montipora capitata

Genomic Location: Sc0000764:44868...63787
NR annotation: CAH3018473.1, unnamed protein product [Porites evermanni]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g17229.t1

atgtttaaaatcaagaatattgtccttacttctttaaagtaccacgaattaaaaggaagcttcttctttgtatcttcgttgcacattgttcgaagaagattttccaaggaaggggaaaatatgtctgggcgatctttgccaaaatggattgctcctgaaggatcaggggaactgaagctgtataacagtcttactcgtgaaaagaatgtgtttgtgccacaaaatggaaggagagttctttggtacagctgtggacctactgtatatgatgcatcacacatggggcatgccaggtcctacattactttcgatattttgcgaagagtccttcagtcatattttaactatgatgtgttctatgtgatgaacatcacagatatcgatgacaagattattttcagagccagaagaaatcatctcttagagaaatacaatgaggagaacaattctccagagaaaattatagaagatgtaaatgctgcccttgagccctatgtagaaaaaatggaaactagtacagatgaagacaagaaaaatatgtatagtagaattattgagaaagtgaaatcctccatgttaaggctaaaagacttgaaggtgtcaaacagtagttttgaatctataaagccagctttggaggaattactgaaagatgcaagtgatccactgtcaacttggttggacttgcagtttggatcaaatgtgacagaacaaaggatatttgcaaaactcacacaacactgggagaatgaattccataaagatatgaaagctctaaatatccttccggcagactgtgtaactcggattacccaatacattcctgaatgtgtcacatttatccagagagttatggacaatggatatgcgtaccattccaatggttcggtgtattttgacaccattaagtttggatctagtgaaaaacactcctatgctagattagtccctgaagctgttggtgatatggaggctcttgctgagggagaaggagaattgagtcagaacccaggtgataagaaatccgagcgggactttgcgctttggaaagctagcaaaccaggcgaacctgcatgggattcaccatggggaaagggtcgaccaggatggcacgtagaatgctccgtcatggcaagtgccattttgggcagctccattgacattcacactggtggagtggatttgaaatttccgcatcatgacaatgaactggcacagtccgaggcccattttggtgtttgccagtggattcattattttctacattcaggacatttgactattgaaggatgtaaaatgtcaaagtctttgaagaacttcatcacaatcaaggaagccttagaaaggaactcagccagacagataagatttgcgttcctcctgcatgcgtggaattcaacgctggattacagtgaaaatgtgcttcgagaagcagagcagacggacaagttgtttaatgattttttcctaaatgttaaagacgtcctacggaaaccggaaggcacatcaccatcttcccataattaccacgaactagaaaaagatcttcaagaaaaatttttggcgaaaaaggcggcggtccatgatgctctttgtgattcgatcgacacgccctctgccatgcggcatctgcaagatcttgtaaaacagaccaatatttacatcagcagcaaaaaggacaaaagggaatcgccaaaccatcaagcgttagagggtattgcaaagtatctcacacatatgttgagggtctttggagctattgaagaagaacaaaccatagggtttccagttgccggcaaaaatgcggcaataaatcacgaggatgttgcgatgccgtatgtccagttattggctgacttcagagatgatatcaggagcattgctcgtgaagaaaaagtaactcgaattcttcaagcatgtgacaaactgagggatgagagtcttccagagcttggtgttaagttagaagacgtcgaaggtggacattctccagtgataaagtttgtagacagagaaacattgttgaaagaaaaacagcaacagttagaggaacaagagaaaaaacggaaacagaaagaggaagccaagaaaaaacttgaagctgaaaaggcagcaaaagaagccaaagcaaagattccaccctgggaaatgttcaaacacgaaacggacaaatattctcagtttgatgaacagggagtccctacgcatgaccaatcgggcgaaccactcagcggcaagctgaccaagaaactgaaaaagatttaccaacaacaggaaaaactttacaactcaacaaggcctggagcaagcgaagcagcgaacggatcgacagaacactga

Transcript

g17229.t1

atgtttaaaatcaagaataTTGTCCTTACTTCTTTAAAGTACCACGAATTAAAAGGAAGCTTCTTCTTTGTATCTTCGTTGCACATTGTTCGAAGAAGATTTTCCAAGGAAGGGGAAAATATGTCTGGGCGATCTTTGCCAAAATGGATTGCTCCTGAAGGATCAGGGGAACTGAAGCTGTATAACAGTCTTACTCGTGAAAAGAATGTGTTTGTGCCACAAAATGGAAGGAGAGTTCTTTGGTACAGCTGTGGACCTACTGTATATGATGCATCACACATGGGGCATGCCAGGTCCTACATTACTTTCGATATTTTGCGAAGAGTCCTTCAGTCATATTTTAACTATGATGTGTTCTATGTGATGAACATCACAGATATCGATGACAAGATTATTTTCAGAGCCAGAAGAAATCATCTCTTAGAGAAATACAATGAGGAGAACAATTCTCCAGAGAAAATTATAGAAGATGTAAATGCTGCCCTTGAGccCTATGTAGAAAAAATGGAAACTAGTACAGATGAAGACAAGAAAAATATGTATAGTAGAATTATTGAGAAAGTGAAATCCTCCATGTTAAGGCTAAAAGACTTGAAGGTGTCAAACAGTAGTTTTGAATCTATAAAGCCAGCTTTGGAGGAATTACTGAAAGATGCAAGTGATCCACTGTCAACTTGGTTGGACTTGCAGTTTGGATCAAATGTGACAGAACAAAGGATATTTGCAAAACTCACACAACACTGGGAGAATGAATTCCATAAAGATATGAAAGCTCTAAATATCCTTCCGGCAGACTGTGTAACTCGGATTACCCAATACATTCCTGAATGTGTCACATTTATCCAGAGAGTTATGGACAATGGATATGCGTACCATTCCAATGGTTCGGTGTATTTTGACACCATTAAGTTTGGATCTAGTGAAAAACACTCCTATGCTAGATTAGTCCCTGAAGCTGTTGGTGATATGGAGGCTCTTGCTGAGGGAGAAGGAGAATTGAGTCAGAACCCAGGTGATAAGAAATCCGAGCGGGACTTTGCGCTTTGGAAAGCTAGCAAACCAGGCGAACCTGCATGGGATTCACCATGGGGAAAGGGTCGACCAGGATGGCACGTAGAATGCTCCGTCATGGCAAGTGCCATTTTGGGCAGCTCCATTGACATTCACACTGGTGGAGTGGATTTGAAATTTCCGCATCATGACAATGAACTGGCACAGTCCGAGGCCCATTTTGGTGTTTGCCAGTGGATTCATTATTTTCTACATTCAGGACATTTGACTATTGAAGGATGTAAAATGTCAAAGTCTTTGAAGAACTTCATCACAATCAAGGAAGCCTTAGAAAGGAACTCAGCCAGACAGATAAGATTTGCGTTCCTCCTGCATGCGTGGAATTCAACGCTGGATTACAGTGAAAATGTGCTTCGAGAAGCAGAGCAGACGGACAAGTTGTTTAATGATTTTTTCCTAAATGTTAAAGACGTCCTACGGAAACCGGAAGGCACATCACCATCTTCCCATAATTACCACGAACTAGAAAAAGATCTTCAAGAAAAatttttggCGAAAAAGGCGGCGGTCCATGATGCTCTTTGTGattcgATCGACACGCCCTCTGCCATGCGGCATCTGCAAGATCTTGTAAAACAGACCAATATTTACATCAGCAGCAAAAAGGACAAAAGGGAATCGCCAAACCATCAAGCGTTAGAGGGTATTGCAAAGTATCTCACACATATGTTGAGGGTCTTTGGAGCTATTGAAGAAGAACAAACCATAGGGTTTCCAGTTGCCGGCAAAAATGCGGCAATAAATCACGAGGATGTTGCGATGCCGTATGTCCAGTTATTGGCTGACTTCAGAGATGATATCAGGAGCATTGCTCGTGAAGAAAAAGtaactCGAATTCTTCAAGCATGTGACAAACTGAGGGATGAGAGTCTTCCAGAGCTTGGTGTTAAGTTAGAAGACGTCGAAGGTGGACATTCTCCAGTGATAAAGTTTGTAGACAGAGAAACattgttgaaagaaaaacagCAACAGTTAGAGGAACAAGAGAAAAAACGGAAACAGAAAGAGGAAGCCAAGAAAAAACTTGAAGCTGAAAAGGCAGCAAAAGAAGCCAAAGCAAAGATTCCACCCTGGGAAATGTTCAAACACGAAACGGACAAATATTCTCAGTTTGATGAACAGGGAGTCCCTACGCATGACCAATCGGGCGAACCACTCAGCGGCAAGCTGACCAAGAAACTGAAAAAGATTTACCAACAACAGGAAAAACTTTACAACTCAACAAGGCCTGGAGCAAGCGAAGCAGCGAACGGATCGACAGAACACTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5F408	Cysteine--tRNA ligase, cytoplasmic OS=Gallus gallus OX=9031 GN=CARS1 PE=2 SV=1
Q4R550	Cysteine--tRNA ligase, cytoplasmic OS=Macaca fascicularis OX=9541 GN=CARS1 PE=2 SV=1
Q5M7N8	Cysteine--tRNA ligase, cytoplasmic OS=Xenopus tropicalis OX=8364 GN=cars1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002378 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01406 all species →	tRNA-synt_1e	tRNA synthetases class I (C) catalytic domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR032678 all species →	Domain	tRNA synthetases class I, catalytic domain	Interproscan
IPR015803 all species →	Family	Cysteine-tRNA ligase	Interproscan
IPR024909 all species →	Family	Cysteinyl-tRNA synthetase/mycothiol ligase	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR009080 all species →	Homologous_superfamily	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10890 all species →	CYSTEINYL-TRNA SYNTHETASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004817 all species →	Molecular Function	cysteine-tRNA ligase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006423 all species →	Biological Process	cysteinyl-tRNA aminoacylation	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	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

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
K01883	CARS, cysS; cysteinyl-tRNA synthetase	EC:6.1.1.16	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 g17229.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

59.4Max TPM

22.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	23.88	55.06
whole organisms · low pH treatment	15	15	20.18	59.45
whole organisms · extra low pH treatment pH treatment	12	12	20.96	47.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	55.06
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	49.86
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	46.75
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	41.65
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	35.24
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	33.78
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	33.47
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	27.98
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	26.02
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	21.41
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	20.60
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	20.09
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	17.77
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	16.63
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	16.45
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	8.25
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	7.39
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	7.33
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	5.97
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	5.17
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	4.56
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	59.45
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	50.95
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	48.45
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	23.01
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	22.88
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	19.07
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	18.76
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	15.11
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	10.17
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	9.58
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	7.53
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	6.99
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	5.61
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	2.60
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	2.49
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	47.34
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	41.45
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	40.75
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	27.13
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	21.74
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	17.43
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	14.73
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	14.01
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	7.19
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	6.98
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	6.68
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	6.15

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.