LXL04_029960 | RubberDandelionOmics

Gene overview

LXL04_029960

Reference: OH-1004 Chr: Chr06 Coordinates: 104033581-104035544 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

654 bp · LXL04_029960|LXL04_029960|OH1004|cDNA

ATGCCATTTGAATCCAATTATGCTGAAAAGTCTCGCCAGACCAACTCTAAAACTTTTGTGAAGACTGTGGAGGAGGCAATGGACGAGGTGAGCAGAAGAAGTGCACTTGGTTTGTCATGCATGTGTAGAAGTAAGCAGAATTTTAGGAAGACTGATGTGGAAGGGTATTATGCTGTTGATATAGCTGATTATGAGCCTGGAGCTGTATACTCAATTGATGCTATTGAGAAAGCTAGGGCTATTAGCATCCCACTAATTCC...

CDS

Download CDS FASTA

654 bp · LXL04_029960|LXL04_029960|OH1004|CDS

ATGCCATTTGAATCCAATTATGCTGAAAAGTCTCGCCAGACCAACTCTAAAACTTTTGTGAAGACTGTGGAGGAGGCAATGGACGAGGTGAGCAGAAGAAGTGCACTTGGTTTGTCATGCATGTGTAGAAGTAAGCAGAATTTTAGGAAGACTGATGTGGAAGGGTATTATGCTGTTGATATAGCTGATTATGAGCCTGGAGCTGTATACTCAATTGATGCTATTGAGAAAGCTAGGGCTATTAGCATCCCACTAATTCC...

Protein

Download Protein FASTA

217 aa · LXL04_029960|LXL04_029960|OH1004|PROTEIN

MPFESNYAEKSRQTNSKTFVKTVEEAMDEVSRRSALGLSCMCRSKQNFRKTDVEGYYAVDIADYEPGAVYSIDAIEKARAISIPLIPDLSFLYLQVGTIGDAATAANFLREYGLIGGLAPAGFNFDAKLRTESTDIEDLFIAHIAGMDTLARGLRNAAKLLEDGSLGYSSFDSPLGAQIEAGKADFELLEKKAMEWGEPIVPSGKQELAEIIFQSTM

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_029960`
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_029960

Location Chr06:104033581-104035544 (-)

Description Similar to XYLA: Xylose isomerase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g57655`	Xylose isomerase.	No verified direct reference in this release
`At5g27650`	Together with PDP2, PDP3 and PDP6, interacts with MSI4/FVE and MSI5 to suppress FLC, MAF4 and MAF5 expression by regulating the function of the PRC2 complex and modulating H3K27me3 level, thereby promoting flowering.	No verified direct reference in this release
`At3g05430`	May influence gene expression by regulating the function of the PRC2 complex and modulating H3K27me3 level.	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_029960 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009908 flower development Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0042732 D-xylose metabolic process Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0009536 plastid Cellular Component

GO:0035098 ESC/E(Z) complex Cellular Component

KEGG gene cross-reference

ath:AT3G05430

ath:AT5G27650

ath:AT5G57655

ttm:Tthe_2492

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.

Plastid0.477

Rank 1 · LXL04_029960 · OH-1004

Cytoplasm0.250

Rank 2 · LXL04_029960 · OH-1004

Nucleus0.189

Rank 3 · LXL04_029960 · OH-1004

Extracellular0.084

Rank 4 · LXL04_029960 · OH-1004

Mitochondrion0.063

Rank 5 · LXL04_029960 · 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.

PF27526.1XylA2_C168-213 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029960	`PF27526.1`	XylA2_C	168	213	1.1e-13	51.9

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
`Q9FKK7`	Arabidopsis thaliana	Xylose isomerase	72.222%	Swiss-Prot	weak database homology
`F4K4D6`	Arabidopsis thaliana	PWWP domain-containing protein 1	59.524%	Swiss-Prot	weak database homology
`Q9MA56`	Arabidopsis thaliana	PWWP domain-containing protein 4	58.228%	Swiss-Prot	weak database homology

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