Gene detail

Detailed information of XP_032240336.2 in Nematostella vectensis

Genomic Location: NC_064035.1:3485746...3490321
NR annotation: XP_032240336.2, medium-chain acyl-CoA ligase ACSF2, mitochondrial [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032384445.2

TGTAACTACCTCCCCGCGTAGTCTCGGTTTTCCTTTGTTAGGCCCGGTTCCTCAATGAGACTAGTCGACAACAGCCACACATAACAAGCATACGGGAATATCTCAAATGATGTCACCGAACTTGAGCTATATACATGTGCCTCATGCGTGCCCGATGGACTCACGCCTCTTACACCAGTATCTTGACATACGTGCTGAACAGAATGCTGGGACTGAGGCCGTTGTGATGTATAATATGCAGATGAGTCGGTCCACTATGACTTACGCCCAGTGGAGAAACAGGTCCGTGTCTCTCGCCGCTTCTCTCCTCGAGTTAGGCGTGTCACGTGGGCAGCACGTGCTTCTAATCGGAGGGAACACCCTCGAGTACATCGTGTTCCTCATGGCACTACATCGCATTGGTGCTCTAGCGATTCTGCTGGGTCCTGGAGACCTCACACCTGCTAACACCGCCCTGCTAAAGACCCTCGACTGTACAGCAATTGCATTTAACCCGGTGATGAAGGAGTCCCAGGAAAGACAGCTGTGGACCGGTCTTAAGGAGCTAACcgacaaaaaaacaaacataatcTTCTTTGGAAACTTCAATTTGGCACCCAGCTTCCTCACTGCTACTAAGATTCACTTGTATGATGACCTTCTGAAGCGAGGGGAGTTACTAGGAGTTGAAGATGTGTTGACCGTCCAGGCTCAAGTCCAAGGCGATGATCCTATTGTTGCATTGGCAACTTCAGGCACGACAGGGATCCCAAAGTTTGTCCAACACACGTCGCATGCCATAGTGAATGTCAAGGGAGGTGAACCCTCAACTGATTCTTCTAAGATGAGTAGGGGAAAGATTATCAGTTTTGTGGATCGTCCAGTATCTTGGATAGGCGGCCTGACACCTTTTTATAACAGCCTTTATTCAGAATCAACTGTGGTTTGGATTCCCACAGAGATAGGATTGTCTAACAACCCGGATATCTCATGTGAGGTAATCCAGCGGGAAAAAGTCATCTCATGGAGTCCTAGCCCATCCTTGATCCCAAGGCTCCAGGAATTGCAATCGAAATATGACCTGAGTAATGTTAAGATAATAGTTATGGCAGGGCAAGCATTGACGGCTGATGACCTTTGGTCTGTCATAGAGGCGTTCCCAGCAGCTTATATTTTCCAGGGGTATGCCTCATCTGAGGGATTGAAGATATCTTTTAGATTACTCAACAAGGATATACAAGAGAAGTCATCTGTCGCTAAAATGCAAGTATTTGCTGGTGTGGAAGTCAAGATAGTTGATACGGATGGTAAGGTCGTTCCTCGGGGGCAACCAGGAGAAATCTGCTGCAGAAGTGAGTGTGTTTTCTTGGGCTATTTAGGGAACCCAGAGGCAACGTCTCGAGTGAAGTCCCCACAAGGATGGCTACACACAGAGGATTTAGGAACCATGGATGACCAAGACATGATTGAGGTTACCGGACGCAAGTCAGAAATCATCAAACGAGCGACTGTCAAGATATTCCCGGGCGAGATCAGGGCAGAGCTTGTAAAGAACCCAATCGTTGCCGACACCATCGTCATCGGTGTCCCTGACAAGATGTTGCACGAGGAGATTTGCGCATGCGTAGTGCTTCGAAAAAATGCATGTGATGACGTGCCCTTGGATGCGCTAGCTGATTGGTGCAACGGGAAGTGGCCGCCGCGAGCCGATGGTTTGAGCTTGAAGCCAAAGTACTTCGTGGTATTCGACGAGTTTCCGATGACACGAAGTGCGAAGCTTGATTTACATGGGATCAAGAAAATAGCTTTGGGAAAGCTCGGACTCGAAGGCAAATGAGCCATCGATTTAACGTCGTCTTTAAAATGACTCTGAAGCAGACTTGGGTGACGAATCTTCTACTGCAGCAAAGAATAAATGAACATTAGATTCACATTAGACTGATTGTAGTAGCGAACTAGCATATAGAATCACTAAGAGGAGGGAGGAAAGATCTCGATTCAAGAGCCCCTCATTCATAGTTaataatttttcatttataCAACACTCAAAaagatccccccccccccgctttTTGCGGGCAGGAAGCTGGCATATAAACTCATTTCTCAAGTTATGACACGGAATTTGCAGACCGAACCAAGCAGACCCAGGCTAAAGGTGGACCATGTAGTACAGTTAACACCTGCggcacagcttttaaaaagcgCTCAGCCGTACGCGCCTTTACCGTGAGCTGGTATGGGTAAAATGTTGCttagaatttttattttattttcaggaCTTTAAAATAGACTGTTGTTCTGCTATTCTGACAGCAAATCAGGCTGTGTAGGTTCTTAGTTATTggttaatgtttttttatatacacaGAACAATTACAACCGTCAGTCACTTTTCAGAATGCATGCTGATAATAACAGTAATCAATAACACAACATGTGTGTAATGCACCAAACATTATGAAAAGTATCAAGTCATGTCCTGacattttatattatataggTTTCACATATAGTCCACAGGCCAATACCCCAAAATTAGCTTTTTGGTACCAAGAAAGGTGACAAAGGCTATCATACCTTTTTGAAATGGTTATTATCTGTAGTTTGTGGAAATTTATGATAGACATTACAAATGAGTAGCTTTGAGTATgtaatcacgtgacaaagtgacgtcattatcCTTTCTATATCATGCTTACTTTATGTACTTGGTagagaaaaaacataaaagaaGACGTTTTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
I3PB37	4-coumarate:CoA ligase 1 OS=Petunia hybrida OX=4102 GN=4CL1 PE=1 SV=1
A0A2H5AIX5	4-coumarate-CoA ligase 1 OS=Narcissus pseudonarcissus OX=39639 GN=4CL1 PE=2 SV=1
Q9LU36	4-coumarate--CoA ligase 4 OS=Arabidopsis thaliana OX=3702 GN=4CL4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002956 (this species only)

Pfam domain

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

InterPro

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

PANTHER

PANTHER term	Description	Source
PTHR42814 all species →	AMP-BINDING DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

No Gene Ontology signature was detected for XP_032240336.2. This gene does have a gene model — the search simply returned no hit.

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 XP_032240336.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_032240336.2 across 48 RNA-seq samples of Nematostella vectensis. 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

39TPM > 0

16Conditions

14.0Max TPM

6.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	9.67	13.80
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	6.06	8.03
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	5.46	5.80
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	6.82	8.02
whole 6 week old aboral regenerate · regenerate uncut	3	3	6.05	7.58
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	2.13	6.40
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	5.52	8.57
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	10.13	14.05
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	5.33	9.13
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	7.80	8.25
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	6.68	7.80
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	5.77	9.14
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	8.90	10.10
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	5.91	8.88
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	4.82	7.45
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	2.74	8.21

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	13.80
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	8.21
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	6.99
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	8.03
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	5.38
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	4.78
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.80
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.28
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.28
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	8.02
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.30
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.15
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	7.58
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	6.19
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	4.36
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	6.40
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	8.57
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	7.99
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	14.05
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	8.81
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.55
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	9.13
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	6.87
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	8.25
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	7.66
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	7.49
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	7.80
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	6.31
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	5.94
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	9.14
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	8.16
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	10.10
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	9.13
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	7.47
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	8.88
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	8.86
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	7.45
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	7.01
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	8.21
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_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.