LXL04_030121 | RubberDandelionOmics

Gene overview

LXL04_030121

Reference: OH-1004 Chr: Chr06 Coordinates: 108592175-108596699 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2214 bp · LXL04_030121|LXL04_030121|OH1004|cDNA

ATGACTATTATATTGTGTACATATTTGCCGGTAATCCCGGCGGCGGGTCGACATAGTGACGATGGCGGACGGTGGTTCGAGgaatttttgtttgttttcaaTTGTAGAAAAATGTCTCGGCCACTCCATCGAGGTGTTTCAGGGGGTGGAAGATTATCAGGAAACATTCAAGATTTCTTagaacaagaagaaaaagacTCTCAGATGAAAGTCAAAACAGAGAATGGAGATTCACATAAAAACCATTTATCCCCTTCACG...

CDS

Download CDS FASTA

2214 bp · LXL04_030121|LXL04_030121|OH1004|CDS

ATGACTATTATATTGTGTACATATTTGCCGGTAATCCCGGCGGCGGGTCGACATAGTGACGATGGCGGACGGTGGTTCGAGGAATTTTTGTTTGTTTTCAATTGTAGAAAAATGTCTCGGCCACTCCATCGAGGTGTTTCAGGGGGTGGAAGATTATCAGGAAACATTCAAGATTTCTTAGAACAAGAAGAAAAAGACTCTCAGATGAAAGTCAAAACAGAGAATGGAGATTCACATAAAAACCATTTATCCCCTTCACG...

Protein

Download Protein FASTA

737 aa · LXL04_030121|LXL04_030121|OH1004|PROTEIN

MTIILCTYLPVIPAAGRHSDDGGRWFEEFLFVFNCRKMSRPLHRGVSGGGRLSGNIQDFLEQEEKDSQMKVKTENGDSHKNHLSPSRNPFNFFNSINSSSKQTPPTNGFIVPDPFSPVTSRNRYKLTLFLLKFSLFLIIILALTGSFWWTISLTTSSRNHTFRGYRRLQEQLVSDLWDIGELSLGPSKDKESEFCLQESENYIPCFNITENLDLGLTMGYENDRHCGPTSKQNCLVLAPHSYKIPHRWPTGRDVIWIDNV...

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_030121`
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_030121

Location Chr06:108592175-108596699 (-)

Description Similar to QUA2: Probable pectin methyltransferase QUA2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g78240`	May be involved in the synthesis of homogalacturonan.	Homogalacturonan synthesis in Arabidopsis thaliana requires a Golgi-localized protein with a putative methyltransferase domain.2007 · DOI: 10.1111/j.1365-313x.2007.03086.x The TUMOROUS SHOOT DEVELOPMENT2 gene of Arabidopsis encoding a putative methyltransferase is required for cell adhesion and co-ordinated plant development.2007 · DOI: 10.1111/j.1365-313x.2007.03123.x The OSU1/QUA2/TSD2-encoded putative methyltransferase is a critical modulator of carbon and nitrogen nutrient balance response in Arabidopsis.2008 · DOI: 10.1371/journal.pone.0001387
`At1g13860`	Probable methyltransferase PMT4.	No verified direct reference in this release
`At2g03480`	Probable methyltransferase PMT5.	No verified direct reference in this release
`At3g23300`	Probable methyltransferase PMT1.	No verified direct reference in this release
`At1g04430`	Probable methyltransferase PMT8.	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_030121 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007155 cell adhesion Biological Process

GO:0009735 response to cytokinin Biological Process

GO:0010289 homogalacturonan biosynthetic process Biological Process

GO:0032259 methylation Biological Process

GO:0048364 root development Biological Process

GO:0048367 shoot system development Biological Process

GO:0000138 Golgi trans cisterna Cellular Component

GO:0000139 Golgi membrane Cellular Component

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G04430

ath:AT1G13860

ath:AT1G78240

ath:AT2G03480

ath:AT3G23300

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.

Golgi apparatus0.734

Rank 1 · LXL04_030121 · OH-1004

Cell membrane0.071

Rank 2 · LXL04_030121 · OH-1004

Endoplasmic reticulum0.070

Rank 3 · LXL04_030121 · OH-1004

Extracellular0.057

Rank 4 · LXL04_030121 · OH-1004

Nucleus0.052

Rank 5 · LXL04_030121 · 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.

PF03141.23Methyltransf_29201-727 aa

PF13649.13Methyltransf_25325-417 aa

PF08241.19Methyltransf_11326-420 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030121	`PF03141.23`	Methyltransf_29	201	727	4e-138	461.9
LXL04_030121	`PF13649.13`	Methyltransf_25	325	417	1.7e-06	29.3
LXL04_030121	`PF08241.19`	Methyltransf_11	326	420	3.4e-08	34.7

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
`Q9C9Q8`	Arabidopsis thaliana	Probable pectin methyltransferase QUA2	63.037%	Swiss-Prot	strong database homology
`Q8GYW9`	Arabidopsis thaliana	Probable methyltransferase PMT4	50.809%	Swiss-Prot	strong database homology
`Q3EC77`	Arabidopsis thaliana	Probable methyltransferase PMT5	52.529%	Swiss-Prot	strong database homology
`Q8H118`	Arabidopsis thaliana	Probable methyltransferase PMT1	36.447%	Swiss-Prot	moderate database homology
`Q940J9`	Arabidopsis thaliana	Probable methyltransferase PMT8	34.578%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card