LXL04_031460 | RubberDandelionOmics

Gene overview

LXL04_031460

Reference: OH-1004 Chr: Chr07 Coordinates: 6252054-6253448 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1395 bp · LXL04_031460|LXL04_031460|OH1004|cDNA

ATGGCAGTAATCGCCCTCAAATGTCCAGCCATCGAGGTAGCCGTGGTTGATATTTCCGTCTCTCGGATCACCGCCTGGAACAGCGACCAACTCCCGATCTATGAACCTGGTCTGGATGATGTCGTTAAGTCATGTCGTGGCAAGAATCTGTTCTTTAGTACCGACGTAGAAAAGCACGTTGCTGAGGCTGACATCATCTTTGTTTCTGTTAACACACCGACAAAAACCCGAGGTCTAGGAGCCGGGAAAGCCGCCGATCT...

CDS

Download CDS FASTA

1395 bp · LXL04_031460|LXL04_031460|OH1004|CDS

ATGGCAGTAATCGCCCTCAAATGTCCAGCCATCGAGGTAGCCGTGGTTGATATTTCCGTCTCTCGGATCACCGCCTGGAACAGCGACCAACTCCCGATCTATGAACCTGGTCTGGATGATGTCGTTAAGTCATGTCGTGGCAAGAATCTGTTCTTTAGTACCGACGTAGAAAAGCACGTTGCTGAGGCTGACATCATCTTTGTTTCTGTTAACACACCGACAAAAACCCGAGGTCTAGGAGCCGGGAAAGCCGCCGATCT...

Protein

Download Protein FASTA

464 aa · LXL04_031460|LXL04_031460|OH1004|PROTEIN

MAVIALKCPAIEVAVVDISVSRITAWNSDQLPIYEPGLDDVVKSCRGKNLFFSTDVEKHVAEADIIFVSVNTPTKTRGLGAGKAADLTYWESAARMIADVSKSDKIVVEKSTVPVKTAEAIEKILTHNSKGVNYQILSNPEFLAEGTAIEDLFAPDRVLIGGRETPAGQRAIKALKDVYANWVPEERILCTNLWSAELSKLAANAFLAQRISSVNAMSALCEATGADVAEVSHAVGKDTRIGHKFLNASVGFGGSCFQKD...

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_031460`
TK1151 ID	TkA08G107900
OH-1004 ID	LXL04_031460
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 96.667 / OH-1004 100.000 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_031460

Location Chr07:6252054-6253448 (-)

Description Similar to UGD5: UDP-glucose 6-dehydrogenase 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g15490`	Involved in the biosynthesis of UDP-glucuronic acid (UDP- GlcA), providing nucleotide sugars for cell-wall polymers.	Down-regulation of UDP-glucuronic acid biosynthesis leads to swollen plant cell walls and severe developmental defects associated with changes in pectic polysaccharides.2011 · DOI: 10.1074/jbc.m111.255695 Cell wall ingrowths in nematode induced syncytia require UGD2 and UGD3.2012 · DOI: 10.1371/journal.pone.0041515

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0443600`	Involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers.	No verified direct reference in this release
`Os12g0443500`	Involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers.	No verified direct reference in this release
`Os03g0757900`	Involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031460 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

GO:0006024 glycosaminoglycan biosynthetic process Biological Process

GO:0006065 UDP-glucuronate biosynthetic process Biological Process

GO:0052546 cell wall pectin metabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0003979 UDP-glucose 6-dehydrogenase activity Molecular Function

GO:0051287 NAD binding Molecular Function

KEGG gene cross-reference

ath:AT5G15490

dosa:Os03g0757900

dosa:Os12g0443500

dosa:Os12g0443600

gmx:548074

osa:4352147

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.

Cytoplasm0.592

Rank 1 · LXL04_031460 · OH-1004

Nucleus0.253

Rank 2 · LXL04_031460 · OH-1004

Mitochondrion0.206

Rank 3 · LXL04_031460 · OH-1004

Peroxisome0.071

Rank 4 · LXL04_031460 · OH-1004

Cell membrane0.056

Rank 5 · LXL04_031460 · 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.

PF03721.22UDPG_MGDP_dh_N10-182 aa

PF00984.25UDPG_MGDP_dh194-288 aa

PF03720.23UDPG_MGDP_dh_C312-436 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031460	`PF03721.22`	UDPG_MGDP_dh_N	10	182	5e-56	190.2
LXL04_031460	`PF00984.25`	UDPG_MGDP_dh	194	288	7.7e-33	113.2
LXL04_031460	`PF03720.23`	UDPG_MGDP_dh_C	312	436	9.6e-33	113.4

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
`Q9LF33`	Arabidopsis thaliana	UDP-glucose 6-dehydrogenase 3	88.147%	Swiss-Prot	strong database homology
`Q2QS13`	Oryza sativa subsp. japonica	UDP-glucose 6-dehydrogenase 5	89.224%	Swiss-Prot	strong database homology
`Q2QS14`	Oryza sativa subsp. japonica	UDP-glucose 6-dehydrogenase 4	88.578%	Swiss-Prot	strong database homology
`Q9AUV6`	Oryza sativa subsp. japonica	UDP-glucose 6-dehydrogenase 3	88.793%	Swiss-Prot	strong database homology

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