Gene detail

Detailed information of XP_068731609.1 in Montipora capricornis

Genomic Location: chr12:23410156...23422306
NR annotation: XP_044163563.1, 4-coumarate--CoA ligase 1-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068875508.1

TGAATTCACCAATTAAAAAGCTTTCTATCGGCTGGAAAACTGTCTGTCAACTTTGAGGCTCACTTAATTGTGGCTTAacttaattttgtcaacatGTTGACTGCTTGATTTGTCCACGCTGTTTGGGGAAGTTAATATGGCCTTGCGAAGCAAATATTCGAACGTACAAATCCCTGTGAACGTTTCATGGCCGGAATTTGTGTTCGAAAACTTCGAAGATTACGAAAACCGCACAGCAATCGTGTGTGGTTCAACGAATACCTCCTACACATTCTCTGAAGTTAAGAATTTCAGCAGAAAGTTTTGTTCTGCGCTGAACCAAAGAGGGATCAAGAAGGGTGATGTCGTAGCCATTTTAGCTCCAAACGTTCCTGAATTTGCTATTGTATTTTTGGGAGTTCTTCAACTCGGCGCCGTTGTGACATCTGTCAATCCACACTTCACAAGCAAAGAACTGATCAATCAGCTTAGAGAGGCCAACGCAAAGTGTATTATCGCTGTTCATCAGTTGGTGCATCGAGCGAAGGAAGCCGAGGAAGAACTGCAAACCGGTCATGTGATCGTCATTGGGGAGGACGATCAATGCGTGTCGCTCTCCGAAATTCTCAACGGAGACGGGGAGATTAGCTCTCCGGTCGTCGAACTGAACCCGGAGGAGGACTTAGCCATTCTGCCATTTTCCTCTGGTTCGTCTGGATTACCGAAGGGAGTTATGATTACGCATCAAAATTTGATCGCTTTGGGTTCCATTGTGAAATCTGAGGGAATGTTGAATTTCAACGAAAATTCTAAAATACTGACCTTAATTCCTTTTTACCGTGCCTTCGGAATGATAGCCGTGCTGTCGATGAGCCTTCGAATGGGAAGCACCTTGATCTCCGTGCCAAGATTCGATGACAACATGCACATGCTCTGTCACCTTCTTCAATATTACAAAGTAACACATCTTATTACGGAGACTTCCACTGTACATCTGCTGGCCAGACAACCAGGAATTGAAAAGTTCCAGCTGTCTTCTCTTACAGAGGTGATATCCACTGCTTGTTTATTAACAGCGGAAATATcgaagaaattacaaaaaagaaTACCTCATTTAAAGAGAATTACTCAATgTTATGGGTTGACTGAAAGTACCGCCGTAAGTCACATGACCCCAGCAACGAATGCAAAGCACGGATCCGTGGGAACATTGCTCCCCAATCTCGAATGTAAGGTCGTTGATCCTAAAACAAAGCAGAATCTTGGTGTAGGTCAACGCGGGGAAATTTGTATCCGAGGACCAACACTAATGAAAGGTTACTTAAATAACCAGAAAGCTTCAGAACTTTCGATCGACCAAGATGGCTGGCTTCACACTGGAGATATAGGTTACTATGACGAAGACGAGCATTTCGTTCTTGTCAACAAGCTCAAAGATCTCATAAAATTCAGAGGACACCAGATCTCGCCCTCCGAGCTGGAAACTCTCCTCAGGGCCCACCCAGGCATAAAGGACGCAGTGGTTGTTGGGATCCCAGACCCTGAGGCGGGCGAAGTACCCATGGCATACGTTGTCAGCAAACATGACGACGAACTTACTGAGATTGAAGTTATGGAATACGTGGACGAAAACGCGGCACCCTATAAAAAATTAAGAGGTGGAGTTGAGTTTATCTCCGCAATTCCCAAAAATATGGATGGGCAAGTCCTTCGGGCTGAGCTTGTTGAGAGGCAAAGAAATGGCAATTCAAGTGCTGTGCTTCGTAGGAGATCGTCGGTCTTGCATGCatggaaagaagagaaaaggtTCTCCATAAAAAGATTCAGTCTTACCCCAAACACCAGGCCAAGGGATATCGGTCCAATCGCCGAAGAAAAACCAGCAACCGCCGCACGATCCCAGAGCTGCGTTTTGTTATAGAAGAATAAGAAAAAGAATATTATTTATTAAGGACCTAATCTCAAGGCGAGTTTGTTTAGATGTGGCTGAAATTTTGATTCGCAACCTGCGTTGAAATTTCGTTTCGATTACATGCTTGTAGGTAGAATTAGGCTGAATAATGAGCCGAGTCGATGTGCATCGAGCTGAAAATTTTACCCCTTGGTTAGCTCAAAGCAGACTGGATTTTCAGCACAGGAACAAACCCTGTTTTGGcacattttcacattttttttttagatatttttttccGAAAAGCGAGATGAATTTTCCAGCTGGGAAAAAATCGACGATAACAAAATGGTTCCTTGCCCCGATCTCATAGCTCACAGGGTGTCCTCGTTTTTTAGCAATTCCACTTGCAAGGATTTCCCTATAagtgaagaaaaacaacaacatatatttctttcaaacattgtCACCAATTTTCAATAACTTCTCCCGAAAATACCTGTTAGTAAAGGAAATCATAACAGGACAACTACGAATACCGCGATGGTACCGGAGATATGGTGCATAAGAAATGCCTATGTTTATGAGAGGAGGGCAGGAAAGTGAAGGTAGACATTTCCCATTGGAAAAAGTGTGTTTTAAGTTGCTTTCAAAAGTATTAAGTAATTTGATTCTTGACAGCGTTTCCTGCCGTATTTTCTAGATGTAGTAACATTTCGGTTTTCGGCTGATTCTTGAGGGCTCTTTGAAAGCAAATTTCTATAAGAAGGCCAACGGACATTTTGAAACGTCGATGGACACTCGAGAGAACTCGAGTATCGCGGAGATGTTCATGTTCACTTAAAGTGCGGTATAAAATAAATGGTCTTCCTTAAAGC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P14912	4-coumarate--CoA ligase 1 OS=Petroselinum crispum OX=4043 GN=4CL1 PE=2 SV=1
I3PB37	4-coumarate:CoA ligase 1 OS=Petunia hybrida OX=4102 GN=4CL1 PE=1 SV=1
P14913	4-coumarate--CoA ligase 2 OS=Petroselinum crispum OX=4043 GN=4CL2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000834 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00501 all species →	AMP-binding	AMP-binding enzyme	Family	Interproscan
PF13193 all species →	AMP-binding_C	AMP-binding enzyme C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042099 all species →	Homologous_superfamily	ANL, N-terminal domain	Interproscan
IPR000873 all species →	Domain	AMP-dependent synthetase/ligase domain	Interproscan
IPR045851 all species →	Homologous_superfamily	AMP-binding enzyme, C-terminal domain superfamily	Interproscan
IPR020845 all species →	Conserved_site	AMP-binding, conserved site	Interproscan
IPR025110 all species →	Domain	AMP-binding enzyme, C-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24096 all species →	LONG-CHAIN-FATTY-ACID--COA LIGASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016405 all species →	Molecular Function	CoA-ligase activity	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
K01904	4CL; 4-coumarate--CoA ligase	EC:6.2.1.12	Phenylpropanoid biosynthesis	ko00940	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068731609.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples

27TPM > 0

1Conditions

15.0Max TPM

6.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	27	6.43	14.96

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	14.96
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	14.93
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	13.06
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	12.64
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	12.44
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	11.27
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	11.14
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	10.58
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	10.09
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	10.01
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	9.94
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	9.84
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	9.70
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	9.34
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	8.94
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	8.14
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	7.70
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	6.20
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	5.87
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	5.85
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	5.10
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	5.08
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	4.77
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	4.72
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	3.37
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	3.19
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	2.77
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.