LXL04_004225 | RubberDandelionOmics

Gene overview

LXL04_004225

Reference: OH-1004 Chr: Chr01 Coordinates: 130085268-130087720 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1785 bp · LXL04_004225|LXL04_004225|OH1004|cDNA

ATGGCCGCCGTTGCTTCTCCCGCAGATCTGACCAATTTCTGTGAAAACAATTGGATTTCCTTTACTTATTTTTCCACAGAAGCTGCCGATTTGTTGAAGAACATGTCATTAGATTCTCAATCCAAGACCCTGGAGACTTCAGAGCCTGCTAAGAAGCCTTCAGTTGAATCCGGCAACAATGGCAACATTCAAAACCAACCTTTTGAAAGGTCTCTCACACCAATCGTTCCAGATACCATGGATCCAACATTGGCTTACTA...

CDS

Download CDS FASTA

1785 bp · LXL04_004225|LXL04_004225|OH1004|CDS

ATGGCCGCCGTTGCTTCTCCCGCAGATCTGACCAATTTCTGTGAAAACAATTGGATTTCCTTTACTTATTTTTCCACAGAAGCTGCCGATTTGTTGAAGAACATGTCATTAGATTCTCAATCCAAGACCCTGGAGACTTCAGAGCCTGCTAAGAAGCCTTCAGTTGAATCCGGCAACAATGGCAACATTCAAAACCAACCTTTTGAAAGGTCTCTCACACCAATCGTTCCAGATACCATGGATCCAACATTGGCTTACTA...

Protein

Download Protein FASTA

594 aa · LXL04_004225|LXL04_004225|OH1004|PROTEIN

MAAVASPADLTNFCENNWISFTYFSTEAADLLKNMSLDSQSKTLETSEPAKKPSVESGNNGNIQNQPFERSLTPIVPDTMDPTLAYYHSGYPSPAYYYGGYDGGATNDWDDYSRYANPDGLDLSHGAYGDNGSLMFPGYGYTPYGPYSPAGSPVPTATHDGQSQLYGAQHYQYPTPYFQPMAQSPAVPPKGDISRSTPAVQDTKVRPPVYQNSVFNRSAPNSFQGFDGPIPWIDGPIRNNTITPPLLNTNGFSSKNQNVR...

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_004225`
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_004225

Location Chr01:130085268-130087720 (-)

Description Similar to ECT2: YTH domain-containing protein ECT2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g13460`	Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability (Probable).	The YTH Domain Protein ECT2 Is an m6A Reader Required for Normal Trichome Branching in Arabidopsis.2018 · DOI: 10.1105/tpc.17.00854 An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis.2018 · DOI: 10.1105/tpc.17.00833 The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis.2018 · DOI: 10.1105/tpc.17.00934
`At1g55500`	Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability (Probable).	An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis.2018 · DOI: 10.1105/tpc.17.00833
`At5g61020`	Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability (Probable).	An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis.2018 · DOI: 10.1105/tpc.17.00833
`At3g03950`	Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and regulates mRNA stability (By similarity).	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_004225 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006402 mRNA catabolic process Biological Process

GO:0007276 gamete generation Biological Process

GO:0007284 spermatogonial cell division Biological Process

GO:0009615 response to virus Biological Process

GO:0009751 response to salicylic acid Biological Process

GO:0019722 calcium-mediated signaling Biological Process

GO:0030155 regulation of cell adhesion Biological Process

GO:0034063 stress granule assembly Biological Process

GO:0043488 regulation of mRNA stability Biological Process

GO:0045087 innate immune response Biological Process

GO:0045746 negative regulation of Notch signaling pathway Biological Process

GO:0048255 mRNA stabilization Biological Process

KEGG gene cross-reference

ath:AT1G55500

ath:AT3G03950

ath:AT3G13460

ath:AT5G61020

bta:541050

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.

Cytoplasm0.641

Rank 1 · LXL04_004225 · OH-1004

Nucleus0.385

Rank 2 · LXL04_004225 · OH-1004

Mitochondrion0.050

Rank 3 · LXL04_004225 · OH-1004

Cell membrane0.045

Rank 4 · LXL04_004225 · OH-1004

Endoplasmic reticulum0.032

Rank 5 · LXL04_004225 · 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.

PF04146.22YTH388-526 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004225	`PF04146.22`	YTH	388	526	2.1e-49	167.4

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
`Q9LJE5`	Arabidopsis thaliana	YTH domain-containing protein ECT2	46.983%	Swiss-Prot	moderate database homology
`A0A1P8AS03`	Arabidopsis thaliana	YTH domain-containing protein ECT4	48.480%	Swiss-Prot	moderate database homology
`F4K1Z0`	Arabidopsis thaliana	YTH domain-containing protein ECT3	66.667%	Swiss-Prot	weak database homology
`Q3MK94`	Arabidopsis thaliana	YTH domain-containing protein ECT1	53.125%	Swiss-Prot	moderate database homology

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