TkA03G047460 | RubberDandelionOmics

Gene overview

TkA03G047460

Reference: TK1151 Chr: Chr03 Coordinates: 12519392-12522030 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1813 bp · TkA03G047460|TK1151|cDNA

TTTCGCTGATTTATCATACACATTAGTCGACAGATCTCTGTAAGCGAAGCAAGCACACACACTCTCTCACGTCTGATCCAGGATCAACCGATCTAACAGATTTCTGGTCTACTGATACACATAGTAAAATGGTGAAGATCTGCTGCATAGGAGCCGGATACGTCGGCGGGCCCACCATGGCAGTCATAGCACTAAAATGCCCCGACATTCAAGTCGCAGTGGTCGATATTTCCGTCCCCCGAATCACCGCCTGGAACAGC...

CDS

Download CDS FASTA

1443 bp · TkA03G047460|TK1151|CDS

ATGGTGAAGATCTGCTGCATAGGAGCCGGATACGTCGGCGGGCCCACCATGGCAGTCATAGCACTAAAATGCCCCGACATTCAAGTCGCAGTGGTCGATATTTCCGTCCCCCGAATCACCGCCTGGAACAGCGACACCCTCCCAATCTACGAACCCGGCCTAGACGACGTCGTGAAACAATGCCGTGGCAAAAACCTCTTCTTCAGCACCGAAGTCGAAAAACACGTATGCGAAGCCGACATAGTCTTCGTCTCAGTCAA...

Protein

Download Protein FASTA

480 aa · TkA03G047460|TK1151|PROTEIN

MVKICCIGAGYVGGPTMAVIALKCPDIQVAVVDISVPRITAWNSDTLPIYEPGLDDVVKQCRGKNLFFSTEVEKHVCEADIVFVSVNTPTKTRGLGAGKAADLTYWESAARMIADVSKSDKIVVEKSTVPVKTAEAIEKILTHNSKGINFQILSNPEFLAEGTAVQDLFHPDRVLIGGRETPGGEKAIATLKSVYAHWVPDHNIITTNLWSAELSKLAANAFLAQRISSVNAMSALCEATGANVNQVAYAVGKDTRIGPK...

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	`TkA03G047460`
TK1151 ID	TkA03G047460
OH-1004 ID	LXL04_006551
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 90.566 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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G047460

Location Chr03:12519392-12522030 (+)

Description Similar to UGD2: UDP-glucose 6-dehydrogenase 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g29360`	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
`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
`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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006551 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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:0099503 secretory vesicle Cellular Component

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

GO:0051287 NAD binding Molecular Function

KEGG gene cross-reference

ath:AT3G29360

ath:AT5G15490

dosa:Os03g0757900

dosa:Os12g0443600

gmx:548074

osa:4352147

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

Open Annotation Module

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.

Cytoplasm0.640

Rank 1 · TkA03G047460 · TK1151

Nucleus0.252

Rank 2 · TkA03G047460 · TK1151

Mitochondrion0.178

Rank 3 · TkA03G047460 · TK1151

Peroxisome0.070

Rank 4 · TkA03G047460 · TK1151

Cell membrane0.055

Rank 5 · TkA03G047460 · TK1151

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.

PF03721UDPG_MGDP_dh_N3-198 aa

PF01488Shikimate_DH22-38 aa

PF03720UDPG_MGDP_dh_C49-87 aa

PF01488Shikimate_DH56-91 aa

PF15219TEX12115-166 aa

PF00984UDPG_MGDP_dh210-304 aa

PF03720UDPG_MGDP_dh_C328-451 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G047460	`PF03721`	UDPG_MGDP_dh_N	3	198	4.1e-65	219.8
TkA03G047460	`PF01488`	Shikimate_DH	22	38	0.36	11.6
TkA03G047460	`PF03720`	UDPG_MGDP_dh_C	49	87	6.5e-32	110.7
TkA03G047460	`PF01488`	Shikimate_DH	56	91	0.36	11.6
TkA03G047460	`PF15219`	TEX12	115	166	0.062	14.3
TkA03G047460	`PF00984`	UDPG_MGDP_dh	210	304	1.2e-32	112.6
TkA03G047460	`PF03720`	UDPG_MGDP_dh_C	328	451	6.5e-32	110.7

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
`Q9LIA8`	Arabidopsis thaliana	sp\|Q9LIA8\|UGDH2_ARATH UDP-glucose 6-dehydrogenase 2	89.400%	Swiss-Prot	High
`Q2QS13`	Oryza sativa subsp. japonica	sp\|Q2QS13\|UGDH5_ORYSJ UDP-glucose 6-dehydrogenase 5	89.000%	Swiss-Prot	High
`Q9AUV6`	Oryza sativa subsp. japonica	sp\|Q9AUV6\|UGDH3_ORYSJ UDP-glucose 6-dehydrogenase 3	88.500%	Swiss-Prot	High
`Q2QS14`	Oryza sativa subsp. japonica	sp\|Q2QS14\|UGDH4_ORYSJ UDP-glucose 6-dehydrogenase 4	88.100%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card