TkA02G113000 | RubberDandelionOmics

Gene overview

TkA02G113000

Reference: TK1151 Chr: Chr02 Coordinates: 29587019-29591296 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2518 bp · TkA02G113000|TK1151|cDNA

TAACCATTTGGGATGAAATAGAAATGTCAAAACATACAATGCATTCATGTTGAGGTGAACCATCCACATGTATAAATATCTGTGTGTATATATCGATCCAGGCGTCGGTTGCCACTCCTTGAGTCTCGCCAGAAATTTCGTGGTTTCTTCTTCATCACCTTTTTGGTCGAGATCTTTCTCTCTTTCGAACACGCAATCTGCTAATTGATCCCGATCCGGAATAAAAGTTTATCTCCGGTATGGCTACATATACTCCAAAG...

CDS

Download CDS FASTA

2007 bp · TkA02G113000|TK1151|CDS

ATGGCTACATATACTCCAAAGAACATCCTTATCACTGGAGCTGCAGGCTTCATAGCTTCTCATGTTGCTAATCGTCTCATAAGAAGCTACCCTGATTACAAGATTGTCGTGCTTGACAAGCTTGATTATTGTTCAAGTCTCAAGAACCTCAACCCCTCCAGATCATCTCCTAACTTCAAATTCGTCAAGGGCGACATCGGGAGTGCAGATCTAGTCAACTACCTCCTGATTACCGAATCCATCGACACCATAATGCACTT...

Protein

Download Protein FASTA

668 aa · TkA02G113000|TK1151|PROTEIN

MATYTPKNILITGAAGFIASHVANRLIRSYPDYKIVVLDKLDYCSSLKNLNPSRSSPNFKFVKGDIGSADLVNYLLITESIDTIMHFAAQTHVDNSFGNSFEFTKNNIYGTHVLLEACKVTGQIRRFIHVSTDEVYGETEEDAIVGNHEASQLLPTNPYSATKAGAEMLVMAYGRSYGLPVITTRGNNVYGPNQFPEKLIPKFILLAMRGKPLPIHGDGSNVRSYLYCEDVAEAFEVILHKGEVGHVYNIGTKRERRVID...

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	`TkA02G113000`
TK1151 ID	TkA02G113000
OH-1004 ID	LXL04_016670
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.900
Protein coverage (%)	TK1151 100.000 / OH-1004 33.534 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

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA02G113000

Location Chr02:29587019-29591296 (+)

Description Similar to RHM1: Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g78570`	Trifunctional enzyme involved in UDP-beta-L-rhamnose biosynthesis, a precursor of the primary cell wall components rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II).	Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion.2007 · DOI: 10.1074/jbc.m610196200 Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis.2008 · DOI: 10.1105/tpc.108.058040 Overexpression of a cytosol-localized rhamnose biosynthesis protein encoded by Arabidopsis RHM1 gene increases rhamnose content in cell wall.2009 · DOI: 10.1016/j.plaphy.2008.10.011
`At3g14790`	Trifunctional enzyme involved in UDP-beta-L-rhamnose biosynthesis, a precursor of the primary cell wall components rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II).	Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion.2007 · DOI: 10.1074/jbc.m610196200
`At1g53500`	Trifunctional enzyme involved in UDP-beta-L-rhamnose biosynthesis, a precursor of the primary cell wall components rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II).	RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis.2004 · DOI: 10.1104/pp.103.034314 Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion.2007 · DOI: 10.1074/jbc.m610196200
`At1g63000`	Bifunctional enzyme involved in dTDP-beta-L-rhamnose biosynthesis.	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_016670 · 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:0009225 nucleotide-sugar metabolic process Biological Process

GO:0010192 mucilage biosynthetic process Biological Process

GO:0010214 seed coat development Biological Process

GO:0010253 UDP-rhamnose biosynthetic process Biological Process

GO:0010315 auxin export across the plasma membrane Biological Process

GO:0019300 rhamnose biosynthetic process Biological Process

GO:0019305 dTDP-rhamnose biosynthetic process Biological Process

GO:0030154 cell differentiation Biological Process

GO:0042127 regulation of cell population proliferation Biological Process

GO:0051555 flavonol biosynthetic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G53500

ath:AT1G63000

ath:AT1G78570

ath:AT3G14790

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.

Cytoplasm0.622

Rank 1 · TkA02G113000 · TK1151

Nucleus0.247

Rank 2 · TkA02G113000 · TK1151

Peroxisome0.136

Rank 3 · TkA02G113000 · TK1151

Mitochondrion0.133

Rank 4 · TkA02G113000 · TK1151

Cell membrane0.050

Rank 5 · TkA02G113000 · 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.

PF00106adh_short7-71 aa

PF05368NmrA7-131 aa

PF04321RmlD_sub_bind8-318 aa

PF01370Epimerase9-251 aa

PF02719Polysacc_synt_29-283 aa

PF16363GDP_Man_Dehyd10-315 aa

PF010733Beta_HSD10-235 aa

PF07993NAD_binding_411-191 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G113000	`PF00106`	adh_short	7	71	0.0024	18.1
TkA02G113000	`PF05368`	NmrA	7	131	0.063	13.6
TkA02G113000	`PF04321`	RmlD_sub_bind	8	318	1.3e-30	107.2
TkA02G113000	`PF01370`	Epimerase	9	251	1.4e-70	238.2
TkA02G113000	`PF02719`	Polysacc_synt_2	9	283	2.5e-28	99.8
TkA02G113000	`PF16363`	GDP_Man_Dehyd	10	315	1.3e-73	249.1
TkA02G113000	`PF01073`	3Beta_HSD	10	235	1.5e-27	97.1
TkA02G113000	`PF07993`	NAD_binding_4	11	191	1e-23	84.6
TkA02G113000	`PF13460`	NAD_binding_10	13	170	0.044	14.4
TkA02G113000	`PF00106`	adh_short	157	177	0.0024	18.1
TkA02G113000	`PF04321`	RmlD_sub_bind	385	557	1.3e-30	107.2
TkA02G113000	`PF16363`	GDP_Man_Dehyd	411	553	1.3e-73	249.1
TkA02G113000	`PF01370`	Epimerase	414	549	1.4e-70	238.2
TkA02G113000	`PF02719`	Polysacc_synt_2	415	476	2.5e-28	99.8
TkA02G113000	`PF00106`	adh_short	436	470	0.0024	18.1
TkA02G113000	`PF07993`	NAD_binding_4	447	537	1e-23	84.6

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
`Q9SYM5`	Arabidopsis thaliana	sp\|Q9SYM5\|RHM1_ARATH Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM1	87.000%	Swiss-Prot	High
`Q9LH76`	Arabidopsis thaliana	sp\|Q9LH76\|RHM3_ARATH Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM3	85.100%	Swiss-Prot	High
`Q9LPG6`	Arabidopsis thaliana	sp\|Q9LPG6\|RHM2_ARATH Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM2	84.000%	Swiss-Prot	High
`Q9LQ04`	Arabidopsis thaliana	sp\|Q9LQ04\|RMLCD_ARATH Bifunctional dTDP-4-dehydrorhamnose 3,5-epimerase/dTDP-4-dehydrorhamnose reductase	83.200%	Swiss-Prot	Low

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