LXL04_034124 | RubberDandelionOmics

Gene overview

LXL04_034124

Reference: OH-1004 Chr: Chr07 Coordinates: 83322424-83325352 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

966 bp · LXL04_034124|LXL04_034124|OH1004|cDNA

ATGAAATTAAAAGCATTCGGAGATAGCAGAGTAGAAAAATTGAAGAGTTTCACGGGAAAATCATACGCAAAGTCTCCAAAATCAAAGTTGCGGATAATCGGGGTCACTACGGCGGTGCTGTTATGGACTTTTGTAGTTCAATTAACAGCAATAGGGGATGCTTGGGGACCTATGGTTTTGAAAGGTTGGGCTTCTCACAGTTCTCTTTCTGCTACTGATTATGATGTCAAATTATTACCCATTGTTCCTGCTAGAGTTCT...

CDS

Download CDS FASTA

966 bp · LXL04_034124|LXL04_034124|OH1004|CDS

ATGAAATTAAAAGCATTCGGAGATAGCAGAGTAGAAAAATTGAAGAGTTTCACGGGAAAATCATACGCAAAGTCTCCAAAATCAAAGTTGCGGATAATCGGGGTCACTACGGCGGTGCTGTTATGGACTTTTGTAGTTCAATTAACAGCAATAGGGGATGCTTGGGGACCTATGGTTTTGAAAGGTTGGGCTTCTCACAGTTCTCTTTCTGCTACTGATTATGATGTCAAATTATTACCCATTGTTCCTGCTAGAGTTCT...

Protein

Download Protein FASTA

321 aa · LXL04_034124|LXL04_034124|OH1004|PROTEIN

MKLKAFGDSRVEKLKSFTGKSYAKSPKSKLRIIGVTTAVLLWTFVVQLTAIGDAWGPMVLKGWASHSSLSATDYDVKLLPIVPARVLPRVSYLLLLLLETCCHIITNWHLPNLVILMIYDMVAIARYLNVSLIVPELDKSSFWADPRELGIGIVPWTKLVIGALLYHSISNIKLTCLNSFQLGLKKESNLESYTPCLQLVSQIFHTTITRYKVILQKNFFNCLFTKFKRFILPLIQRYKNDGQPFDLQKLRCRVNFSALK...

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_034124`
TK1151 ID	TkA08G362630
OH-1004 ID	LXL04_034124
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	98.300
Protein coverage (%)	TK1151 95.161 / OH-1004 36.760 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_034124

Location Chr07:83322424-83325352 (+)

Description Similar to RRT1: Rhamnogalacturonan I rhamnosyltransferase 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g15740`	Glycosyltransferase involved in the formation of rhamnogalacturonan I (RG-I) oligosaccharides in the seed coat mucilage, which is a specialized cell wall with abundant RG-I.	Pectin RG-I rhamnosyltransferases represent a novel plant-specific glycosyltransferase family.2018 · DOI: 10.1038/s41477-018-0217-7
`At3g02250`	Glycosyltransferase involved in the formation of rhamnogalacturonan I (RG-I) oligosaccharides in the seed coat mucilage, which is a specialized cell wall with abundant RG-I (By similarity).	No verified direct reference in this release
`At1g14020`	Glycosyltransferase involved in the formation of rhamnogalacturonan I (RG-I) oligosaccharides in the seed coat mucilage, which is a specialized cell wall with abundant RG-I (By similarity).	No verified direct reference in this release
`At2g03280`	Glycosyltransferase involved in the formation of rhamnogalacturonan I (RG-I) oligosaccharides in the seed coat mucilage, which is a specialized cell wall with abundant RG-I (By similarity).	No verified direct reference in this release
`At5g01100`	Glycosyltransferase required for normal cell adhesion and cell wall integrity.	The FRIABLE1 gene product affects cell adhesion in Arabidopsis.2012 · DOI: 10.1371/journal.pone.0042914

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_034124 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006004 fucose metabolic process Biological Process

GO:0007155 cell adhesion Biological Process

GO:0010214 seed coat development Biological Process

GO:0010395 rhamnogalacturonan I metabolic process Biological Process

GO:0045489 pectin biosynthetic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0080157 regulation of plant-type cell wall organization or biogenesis Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT1G14020

ath:AT2G03280

ath:AT3G02250

ath:AT5G01100

ath:AT5G15740

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.

Endoplasmic reticulum0.466

Rank 1 · LXL04_034124 · OH-1004

Golgi apparatus0.219

Rank 2 · LXL04_034124 · OH-1004

Nucleus0.163

Rank 3 · LXL04_034124 · OH-1004

Cytoplasm0.131

Rank 4 · LXL04_034124 · OH-1004

Cell membrane0.085

Rank 5 · LXL04_034124 · 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.

PF10250.16O-FucT118-278 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_034124	`PF10250.16`	O-FucT	118	278	2.6e-12	47.8

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
`Q4V398`	Arabidopsis thaliana	Rhamnogalacturonan I rhamnosyltransferase 1	37.607%	Swiss-Prot	moderate database homology
`Q93ZR8`	Arabidopsis thaliana	Rhamnogalacturonan I rhamnosyltransferase 1	35.714%	Swiss-Prot	moderate database homology
`Q6NQ51`	Arabidopsis thaliana	Rhamnogalacturonan I rhamnosyltransferase 1	33.333%	Swiss-Prot	moderate database homology
`Q6E279`	Arabidopsis thaliana	Rhamnogalacturonan I rhamnosyltransferase 4	31.546%	Swiss-Prot	moderate database homology
`Q9LFC6`	Arabidopsis thaliana	Protein FRIABLE 1	29.911%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card