LXL04_030031 | RubberDandelionOmics

Gene overview

LXL04_030031

Reference: OH-1004 Chr: Chr06 Coordinates: 106096675-106098114 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1440 bp · LXL04_030031|LXL04_030031|OH1004|cDNA

ATGGAGCTCTCCTCTTTGCCCCTCCACCGTCGCCTCCAAATCATCGTCTTTGCCCTCTTCTGCTCCACCTTCCTCCTCCACGCTACCACCGTTGTATACCACCAACTTAACACTGCAGGAGTCCTCCGCTTTCTCTCCGCCCACCTCCTCTTAACCACTATAACATCCCTATCCGCCGCCTTCCTCCTCTGCCTCCATCTCCGCTCCCGAGCTTACCCCGTCTTCCTCCTCAACTACTCCTGCTACCAACCACCGGCGGA...

CDS

Download CDS FASTA

1440 bp · LXL04_030031|LXL04_030031|OH1004|CDS

ATGGAGCTCTCCTCTTTGCCCCTCCACCGTCGCCTCCAAATCATCGTCTTTGCCCTCTTCTGCTCCACCTTCCTCCTCCACGCTACCACCGTTGTATACCACCAACTTAACACTGCAGGAGTCCTCCGCTTTCTCTCCGCCCACCTCCTCTTAACCACTATAACATCCCTATCCGCCGCCTTCCTCCTCTGCCTCCATCTCCGCTCCCGAGCTTACCCCGTCTTCCTCCTCAACTACTCCTGCTACCAACCACCGGCGGA...

Protein

Download Protein FASTA

479 aa · LXL04_030031|LXL04_030031|OH1004|PROTEIN

MELSSLPLHRRLQIIVFALFCSTFLLHATTVVYHQLNTAGVLRFLSAHLLLTTITSLSAAFLLCLHLRSRAYPVFLLNYSCYQPPADRKCTYDMANDFILHGARFTSPEPVEFMRNIYRKSGLGNDTYAPPFMFEEGQIPTMKSSIQEAEEGIFSVVDSLLSKTQILPEEIDAVIVTCGCFSPSPSLSSLIVNHYNLNPDVKTYNLSGMGCSSGVISIDLAAQILRGGGRKIRNVLVVVTENITLNWYEGEDRSMLVTNC...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_030031`
TK1151 ID	TkA07G371840
OH-1004 ID	LXL04_030031
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	96.200
Protein coverage (%)	TK1151 100.000 / OH-1004 76.409 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_030031

Location Chr06:106096675-106098114 (-)

Description Similar to KCS1: 3-ketoacyl-CoA synthase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g01120`	Contributes to cuticular wax and suberin biosynthesis.	KCS1 encodes a fatty acid elongase 3-ketoacyl-CoA synthase affecting wax biosynthesis in Arabidopsis thaliana.1999 · DOI: 10.1046/j.1365-313x.1999.00352.x Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides.2004 · DOI: 10.1073/pnas.0404600101 Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases.2006 · DOI: 10.1016/j.bbrc.2006.05.162
`At2g26640`	Active on both saturated and mono-unsaturated acyl chains C16 to C20.	Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases.2006 · DOI: 10.1016/j.bbrc.2006.05.162
`At1g04220`	Mediates the synthesis of VLCFAs from 22 to 26 carbons in length (e.g. C22, C24, C26).	Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides.2004 · DOI: 10.1073/pnas.0404600101 The DAISY gene from Arabidopsis encodes a fatty acid elongase condensing enzyme involved in the biosynthesis of aliphatic suberin in roots and the chalaza-micropyle region of seeds.2009 · DOI: 10.1111/j.1365-313x.2008.03674.x Two Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynthesis, but differentially controlled by osmotic stress.2009 · DOI: 10.1111/j.1365-313x.2009.03973.x
`At1g19440`	3-ketoacyl-CoA synthase 4.	No verified direct reference in this release
`At2g46720`	Contributes to cuticular wax and suberin biosynthesis (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030031 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000038 very long-chain fatty acid metabolic process Biological Process

GO:0006633 fatty acid biosynthetic process Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009409 response to cold Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009611 response to wounding Biological Process

GO:0010025 wax biosynthetic process Biological Process

GO:0010345 suberin biosynthetic process Biological Process

GO:0030497 fatty acid elongation Biological Process

GO:0042761 very long-chain fatty acid biosynthetic process Biological Process

GO:0070417 cellular response to cold Biological Process

GO:0160062 cutin-based cuticle development Biological Process

KEGG gene cross-reference

ath:AT1G01120

ath:AT1G04220

ath:AT1G19440

ath:AT2G26640

ath:AT2G46720

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Endoplasmic reticulum0.787

Rank 1 · LXL04_030031 · OH-1004

Cell membrane0.077

Rank 2 · LXL04_030031 · OH-1004

Cytoplasm0.058

Rank 3 · LXL04_030031 · OH-1004

Lysosome / Vacuole0.046

Rank 4 · LXL04_030031 · OH-1004

Golgi apparatus0.044

Rank 5 · LXL04_030031 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF08392.19FAE1_CUT1_RppA68-356 aa

PF08541.17ACP_syn_III_C375-456 aa

PF02797.22Chal_sti_synt_C378-455 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030031	`PF08392.19`	FAE1_CUT1_RppA	68	356	2.9e-105	352.5
LXL04_030031	`PF08541.17`	ACP_syn_III_C	375	456	6.6e-11	42.9
LXL04_030031	`PF02797.22`	Chal_sti_synt_C	378	455	7.2e-07	30.0

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9MAM3`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 1	46.209%	Swiss-Prot	moderate database homology
`O48780`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 11	43.871%	Swiss-Prot	moderate database homology
`Q5XEP9`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 2	42.647%	Swiss-Prot	moderate database homology
`Q9LN49`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 4	43.409%	Swiss-Prot	moderate database homology
`Q9ZUZ0`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 13	46.411%	Swiss-Prot	moderate database homology

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