Gene detail

Detailed information of CAB4006826.1 in Paramuricea clavata

Genomic Location: pcla8_s005734:12351...16002
NR annotation: CAB4006826.1, sphingolipid C9-methyltransferase-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-PACLA_8A085002

GATAACTCGCAAACAAGGAGTCGCGTACATTATTCTAGCATCATTCGTGGCTTGCCTTGAGACAGGCGTTTCGAAATATGGACGCTACAACGAAGAACGGTTATGTTTCTCACTCAAATGGAAACCACGCTCATTCAAATGGTTTTCACAAAGCGACCTCAAGTGCTATCAAAAATCTACCCTGGTACAACGTATCGTACAAAACCTTGTTCGCTTTAATCCTCGGGATCCCTGCCCTAATAATCTACCTCGTTCGTCTACCGTGGTGGTTTTATCCAGTCGTAGCGCTCCTGTGCGTTCTCCCGATTTTTCTTTCGTTTATTTTGGTTTTCAATTACTTAAGAATCGGGCGTCAAACAAAGCCGTCGAGGTTGGCCGATTTTGTTGAATTCCGCGATGCCTCGTTTGGCAAAACGTACGCGTCGAAAATGATTCCTTTGGAAACGTTAGTCGAAGCTTATGCGGACGAGAAGGTCGATTTCAAGGGCGATGTGTTAGAATGTTTCGAGCAGCGAGAACGGTTCGCGTGTTTCGCTCTCACTTGGAATCATGTCAAAATATTTTGCTGTAATTTTCTGCCTGAGTTACTAAGTCATTCGCGCTTACAAGATTTGGACCAAGTCCGAGACCACTACGATCGCGGGAACGATTTCTACGAGGCGTTCTTAGGGCCCATGATGGTCTACACGGCTGGATTTTTACGCAAACACGGCGATACTTTGGAAGAGTTACAAACTAATAAACTGAACAAAGTCTGCGATAAGATCGCGCTGAAGCCTGGTGACAAGATGCTGGACATTGGGTGTGGATGGGGAACGCTTGTGAACTTTGCGGCGGGAGAACGCGGGGCAAATGCGGCCGGAGTATCGATCAGTAAAAACCAAGTTGGATATGCCAGAGGTGTTGCGGAAAAAAAGGACCTAAACGCGAAGGCTAGTTTCATGTGTATTGATTACCGAGATATCCCGCAAGAGAGCTACGACAAAATAACCTGTCTGGAAATGGCCGAACATGTTGGAATACTACATTTCCAATCGTTCTTGTGTCAAGTCCGGGATCTCCTTAAAGATGACGGCGTGTTCTTTCTACAGATCGCTGGCCTTCGTCGTGCATTTCAGTGGGAAGATTTCGTATGGGGTCTGTTCATGGATAAGTACGTCTTTCCCGGAGCGGATGCGAGCTGCCCGTTGAGTTTTGTCGTCCAACAACTGGAagcggccggatttgaaattgcCAACGTCGAGACCATCGGGATCCATTATTCCTACACCATCCATCGATGGTACAAGAATTGGGTGCGACCCGATGTGAAAGCTAGCATTTCGGCGAAGTATGGCGTAAGGTTGTACCGAATCTGGGAGGTTTTCCTTGCCTGGTCGACCATTATCGCCCGTCAAGGTAGCTCGACGTGTTTCCAAATTGTCTGTCATAAAAATCTCAACGACTACGACAGGAGTAAGTACTTCTCCATTAAGAAAGAATAAATTATAATGCACCACCGCTAATATATGTAAGCCCTCGAATATTGGTACCGTTTTTGTGAAATTTGAATATAGTGAAAATAAATAACGAATTTTGGCTTTCAAAGGTACTGAAATTATATTTGCCTCTCCACTTGAGAGTTTATCTTAGTTTTCAGTCGTCTTTTCTTGTTTCCTATaccgtccgccatcttgaattttgtcTCACCATATGCATATTGCGTCACAAAGAAAGTATGCCGGAAAAAGATGGCATTTGGCAAGTTTTTGAACGTTCTTTCGAACGAATAGTCTTTATAGTTAATTGAGTTTATCGTGTTACCAAGTCAACAATACATTGCTTCATATTGACGTTGTGATTTGGCCatgaatatattataattaaatttatagtaTAATCAAGTTAAATTTTCCCCCTTTCGTTACCACGTAGGATTTGCAAATATTAAGCGGTGGTGACTGTTCTATCCGAATCAATCAGAATTTAAATGTTATGAGAATTTTAGTTGTAGCCCagtagatatatagatatatatatagccaaAAAACGAACTATTTTTGTGAAGGTTTATAGTTCATGTAAGCTGAAATTTACTATTTGAATTGCTTGTTAATGTTAGCATCTAAATTTTAGTGGGCTGAGTTTGTAGAATGTAGATTAAATTGGCATTTTCATAACAGGATTTtgcatatttacaattttaaagCATTTTTCGTTGACTTGTGGGTTTAATTAGACTTCATTTTGTTAATTTGCTGCCGATTGAAGTAGTTTCATAGAGTTTAATCATGCATAGTTGATATGGAAAATTGACATATGGTTAGTAAGGCCAGTTAAAAACTGAAGACTGTTTTACAAAcatgatgttgaaaatgcatCAACTAAGCTTTTAtcccaagcaaaaaaatattgcaGTTGAAAACAGCCAAGTTGCTATTGAATAATTGTTTCGAGACAAGGAAACAGatttgtttatttattcatttatttatttattacgtTCATTCGTGATGAAAGTGCACAAAAATTATATGAAAGTGAAAAAAACATGAGACAGCATAAAACCATGCGGACTTTTCGCGTCCCTTTATGGCTTGACGTCGTTTTCCATTGTTACAATGGGATCAAGTACGGAAGTCCCTGTAAATATGGGGCGGGCTCCCCTCCCTTTAACTTGTTGGAACTGTTAAGAATTTCATCTATACCGTGGTACAGTATAAAGTGAATCAGACGGGTCATTCCAGGGGATGTTGCTGGTTCAACTCCAATAGGAATGCAAGCTGAAACACTCAGACTGTCGTGTATGGTGAATTTCAAATACCGTTCTGTTCGGTAAGACCTACACTGTAATTCTACACTTTTTAATGTAGTTTGTTTCTGTGGATTGGTAAAAGTGAAAATAATATGATATTGCTTGTAAACTCTAGCATAGTGAGCTACGAGTTTGTGTTGAGAccgtatatattaatatttcaatTACTACGAATAATGATTATCGAATCAATGATTCCAATGATGATGTCATTGGACGATTGCTTCGTCATGCCAAAAATACATTGTCGcataaacatgaacaaaaagTAAAACAATGGCTTTCGCCACATGGTTTAATAGAAAAGATGTTTGAAGATTCATTAGAATTACAATATAACTTATTATCGTTTTGTTTCAGGTTTATTCAGAAATGTGGTCTCTCACCGTCatgtgcgtattgtatttttaaccaaccaaccaatagcaatgttttaagaAAGTAATCTGACTTGGGTAACTTAAAGATTTCTTAAAATCGAAAACACAATACGCACATGACAACCGCGAAGtgccacatttttgcataaaagttgactaacatagataatgaattctattgttattctaatgagtttcgcCGAACCTATTTATATTCTATTAACAACACTTTCGTAGATTTTCCAGACCATATATCGATTGACCAGGACTGTAGAAGTAGTTTACAATTGCGTTAGTTTTTAAACGCCTACAGAATGACTATTAAAAACAATCTAACTATTGTAAATCTTAGTATCGGTGGACAAAAACATTCTTATAATTATGTGTAGAAGATTTTGAACGGCGCCACGTTCGTGCAAATTGTAAACTATAACTTATGGCAAACTGTGTTTCTGTGCAATAAAAATCTGATTTTGTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
I1RNL0	Sphingolipid C9-methyltransferase 2 OS=Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) OX=229533 GN=MT2 PE=3 SV=1
C4R7Z3	Sphingolipid C9-methyltransferase OS=Komagataella phaffii (strain GS115 / ATCC 20864) OX=644223 GN=PAS_chr4_0465 PE=1 SV=1
A0A1U8QYZ5	Sphingolipid C9-methyltransferase A OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=smtA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008476 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02353 all species →	CMAS	Mycolic acid cyclopropane synthetase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR052290 all species →	Family	Sphingolipid C9-methyltransferase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45197 all species →	SYNTHASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_7G04190)-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0071216 all species →	Biological Process	cellular response to biotic stimulus	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
K20238	E2.1.1.317; sphingolipid C9-methyltransferase	EC:2.1.1.317	Enzymes with EC numbers	-	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of CAB4006826.1 across 21 RNA-seq samples of Paramuricea clavata. 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.

21Samples

19TPM > 0

4Conditions

35.2Max TPM

8.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	6	13.13	35.21
apical branchlet · Temperature treatment at T0	6	5	5.53	8.99
apical branchlet · Temperature treatment at T25	5	4	7.36	15.35
apical branchlet · Control at T0	4	4	8.24	11.13

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	35.21
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.90
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.88
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.74
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.62
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	8.44
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	8.99
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	7.94
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.62
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	5.98
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	3.64
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	15.35
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	10.75
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	8.41
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	2.30
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	11.13
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	9.86
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	9.03
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	2.93

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 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.