LXL04_005936 | RubberDandelionOmics

Gene overview

LXL04_005936

Reference: OH-1004 Chr: Chr01 Coordinates: 175909794-175911965 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1962 bp · LXL04_005936|LXL04_005936|OH1004|cDNA

ATGTCATCTGAATCAGCTCCAAAAACAATACTAATCACTGGTGCAGCCGGATTCATAGCCTCCCATGTCACCAAACGTCTTGTGTCAAACTACCCAAATTACAAAATTGTCGCTCTTGACAAGCTTAGTTATTGCTCAAGCCTCAAGAATCTTCAGCCATGTTTCGCATCTTCAAGATTCAAGTTTGTCAAGGCGGATATCGCAAGTTCGGATCTCATCAACTACCTATTGGATGCAGAAGAAATCGACACGATTATGCA...

CDS

Download CDS FASTA

1962 bp · LXL04_005936|LXL04_005936|OH1004|CDS

ATGTCATCTGAATCAGCTCCAAAAACAATACTAATCACTGGTGCAGCCGGATTCATAGCCTCCCATGTCACCAAACGTCTTGTGTCAAACTACCCAAATTACAAAATTGTCGCTCTTGACAAGCTTAGTTATTGCTCAAGCCTCAAGAATCTTCAGCCATGTTTCGCATCTTCAAGATTCAAGTTTGTCAAGGCGGATATCGCAAGTTCGGATCTCATCAACTACCTATTGGATGCAGAAGAAATCGACACGATTATGCA...

Protein

Download Protein FASTA

653 aa · LXL04_005936|LXL04_005936|OH1004|PROTEIN

MSSESAPKTILITGAAGFIASHVTKRLVSNYPNYKIVALDKLSYCSSLKNLQPCFASSRFKFVKADIASSDLINYLLDAEEIDTIMHFAAETHVDNSFGNSFEFTTNNIYGTHVLLEACKVTRRINRFIHVSTDEVYGESDLETDIGNPEASQLLPTNPYSATKAGAEMLVMAYHRSYGLPIITTRGNNVYGPNQFPEKLIPKFVLLAMRGDPLPIHGNGSNVRSYLFCADVAEAFDVILHKGVIGHVYNIGTKRERSVV...

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_005936`
TK1151 ID	TkA01G006290
OH-1004 ID	LXL04_005936
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005936

Location Chr01:175909794-175911965 (+)

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_005936 · GCA_047496595.1_OSU_TarKok_2.0.

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.

Cytoplasm0.612

Rank 1 · LXL04_005936 · OH-1004

Nucleus0.271

Rank 2 · LXL04_005936 · OH-1004

Peroxisome0.129

Rank 3 · LXL04_005936 · OH-1004

Mitochondrion0.128

Rank 4 · LXL04_005936 · OH-1004

Cell membrane0.050

Rank 5 · LXL04_005936 · 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.

PF04321.24RmlD_sub_bind9-318 aa

PF01370.28Epimerase10-252 aa

PF02719.22Polysacc_synt_210-281 aa

PF16363.12GDP_Man_Dehyd11-315 aa

PF01073.263Beta_HSD11-235 aa

PF07993.19NAD_binding_412-192 aa

PF04321.24RmlD_sub_bind369-527 aa

PF16363.12GDP_Man_Dehyd398-533 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005936	`PF04321.24`	RmlD_sub_bind	9	318	2.9e-29	102.8
LXL04_005936	`PF01370.28`	Epimerase	10	252	7.7e-68	229.2
LXL04_005936	`PF02719.22`	Polysacc_synt_2	10	281	1.6e-26	93.9
LXL04_005936	`PF16363.12`	GDP_Man_Dehyd	11	315	3.9e-70	237.7
LXL04_005936	`PF01073.26`	3Beta_HSD	11	235	1.6e-23	83.8
LXL04_005936	`PF07993.19`	NAD_binding_4	12	192	1e-22	81.3
LXL04_005936	`PF04321.24`	RmlD_sub_bind	369	527	2.9e-29	102.8
LXL04_005936	`PF16363.12`	GDP_Man_Dehyd	398	533	3.9e-70	237.7
LXL04_005936	`PF01370.28`	Epimerase	399	521	7.7e-68	229.2
LXL04_005936	`PF02719.22`	Polysacc_synt_2	399	462	1.6e-26	93.9

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	Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM1	72.523%	Swiss-Prot	strong database homology
`Q9LH76`	Arabidopsis thaliana	Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM3	72.727%	Swiss-Prot	strong database homology
`Q9LPG6`	Arabidopsis thaliana	Trifunctional UDP-glucose 4,6-dehydratase/UDP-4-keto-6-deoxy-D-glucose 3,5-epimerase/UDP-4-keto-L-rhamnose-reductase RHM2	72.576%	Swiss-Prot	strong database homology
`Q9LQ04`	Arabidopsis thaliana	Bifunctional dTDP-4-dehydrorhamnose 3,5-epimerase/dTDP-4-dehydrorhamnose reductase	72.028%	Swiss-Prot	weak database homology

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