LXL04_026546 | RubberDandelionOmics

Gene overview

LXL04_026546

Reference: OH-1004 Chr: Chr05 Coordinates: 128042131-128043596 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1302 bp · LXL04_026546|LXL04_026546|OH1004|cDNA

ATGACTTCTTTGAAGCCCATTCTCTCTCACATCGACAACATCCCGTCGACGCCCGGAAAATTTAAGCCGGACAAATCATCTCTGTATTACCTTCACCACCGTTTCCGTCTCCATAGTACCCTCCCCAGAATAGCATTTTGGACGCTCGTTTTCCTGGCTTTTATCTCTGTATTCTTTTTTATGTCGCCTCCTTCCACCACCGCCCCTCGCCGCGGCCTCCGCACCACCGCTTCATACGGCGGATCGGGTTGGGAGAATCA...

CDS

Download CDS FASTA

1302 bp · LXL04_026546|LXL04_026546|OH1004|CDS

ATGACTTCTTTGAAGCCCATTCTCTCTCACATCGACAACATCCCGTCGACGCCCGGAAAATTTAAGCCGGACAAATCATCTCTGTATTACCTTCACCACCGTTTCCGTCTCCATAGTACCCTCCCCAGAATAGCATTTTGGACGCTCGTTTTCCTGGCTTTTATCTCTGTATTCTTTTTTATGTCGCCTCCTTCCACCACCGCCCCTCGCCGCGGCCTCCGCACCACCGCTTCATACGGCGGATCGGGTTGGGAGAATCA...

Protein

Download Protein FASTA

433 aa · LXL04_026546|LXL04_026546|OH1004|PROTEIN

MTSLKPILSHIDNIPSTPGKFKPDKSSLYYLHHRFRLHSTLPRIAFWTLVFLAFISVFFFMSPPSTTAPRRGLRTTASYGGSGWENQVKASAKIRSRNGHSVLVTGAAGFVGAHASLALKRRGDGVVGLDNFNSYYDITLKKSRKSQLLDRAGVFVIDGDINDAVLLRKLFGLVHFTHVLHLAAQAGVRYAMVNPNSYIKSNVDGFVNLLEVAKSTNPQPAIVWASSSSVYGLNSKVPFSEKDRTDQPASLYAATKKAGE...

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_026546`
TK1151 ID	TkA06G005950
OH-1004 ID	LXL04_026546
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 95.682 / OH-1004 97.229 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

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Basic Information and Functional Annotation

Gene ID LXL04_026546

Location Chr05:128042131-128043596 (-)

Description Similar to GAE2: UDP-glucuronate 4-epimerase 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g02000`	Involved in the synthesis of the negatively charged monosaccharide that forms the backbone of pectic cell wall components.	No verified direct reference in this release
`At4g00110`	Involved in the synthesis of the negatively charged monosaccharide that forms the backbone of pectic cell wall components.	No verified direct reference in this release
`At2g45310`	Involved in the synthesis of the negatively charged monosaccharide that forms the backbone of pectic cell wall components.	No verified direct reference in this release
`At4g12250`	Involved in the synthesis of the negatively charged monosaccharide that forms the backbone of pectic cell wall components.	No verified direct reference in this release
`At3g23820`	Involved in the synthesis of the negatively charged monosaccharide that forms the backbone of pectic cell wall components.	Identification and characterization of a UDP-D-glucuronate 4-epimerase in Arabidopsis.2004 · DOI: 10.1016/j.febslet.2004.06.005

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026546 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0033481 galacturonate biosynthetic process Biological Process

GO:0050829 defense response to Gram-negative bacterium Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0000138 Golgi trans cisterna Cellular Component

GO:0005768 endosome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005797 Golgi medial cisterna Cellular Component

GO:0005802 trans-Golgi network Cellular Component

GO:0016020 membrane Cellular Component

GO:0032580 Golgi cisterna membrane Cellular Component

GO:0016854 racemase and epimerase activity Molecular Function

GO:0050378 UDP-glucuronate 4-epimerase activity Molecular Function

KEGG gene cross-reference

ath:AT1G02000

ath:AT2G45310

ath:AT3G23820

ath:AT4G00110

ath:AT4G12250

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.

Golgi apparatus0.576

Rank 1 · LXL04_026546 · OH-1004

Endoplasmic reticulum0.097

Rank 2 · LXL04_026546 · OH-1004

Lysosome / Vacuole0.070

Rank 3 · LXL04_026546 · OH-1004

Plastid0.060

Rank 4 · LXL04_026546 · OH-1004

Cytoplasm0.050

Rank 5 · LXL04_026546 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF01370.28Epimerase102-339 aa

PF04321.24RmlD_sub_bind102-285 aa

PF02719.22Polysacc_synt_2102-226 aa

PF16363.12GDP_Man_Dehyd103-419 aa

PF01073.263Beta_HSD103-385 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026546	`PF01370.28`	Epimerase	102	339	5.6e-49	167.4
LXL04_026546	`PF04321.24`	RmlD_sub_bind	102	285	5.2e-11	42.9
LXL04_026546	`PF02719.22`	Polysacc_synt_2	102	226	7.4e-08	32.6
LXL04_026546	`PF16363.12`	GDP_Man_Dehyd	103	419	1.4e-45	156.9
LXL04_026546	`PF01073.26`	3Beta_HSD	103	385	7.9e-12	45.5

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
`Q9LPC1`	Arabidopsis thaliana	UDP-glucuronate 4-epimerase 2	72.422%	Swiss-Prot	strong database homology
`O81312`	Arabidopsis thaliana	UDP-glucuronate 4-epimerase 3	72.315%	Swiss-Prot	strong database homology
`O22141`	Arabidopsis thaliana	UDP-glucuronate 4-epimerase 4	70.519%	Swiss-Prot	strong database homology
`Q9STI6`	Arabidopsis thaliana	UDP-glucuronate 4-epimerase 5	70.784%	Swiss-Prot	strong database homology
`Q9LIS3`	Arabidopsis thaliana	UDP-glucuronate 4-epimerase 6	72.384%	Swiss-Prot	strong database homology

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