LXL04_012085 | RubberDandelionOmics

Gene overview

LXL04_012085

Reference: OH-1004 Chr: Chr03 Coordinates: 6118942-6122606 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1860 bp · LXL04_012085|LXL04_012085|OH1004|cDNA

ATGCCAGGCATACCTTTAGTTTCTCGTGAAGTCAATTACTCCAGAGACTCGGATCAGATGTGTCGCCAAGAACCTCGTGTTCTTTTGTCTCCGGAAGAGCAAATTGCAGCTGAAGAAACCCTTTCAGTTTACTGCAAGCCTGTTGAACTCTACAACATTCTTCAACGCCGTGctatcaaaagtCCATTGTTTATTCAAAGATGTTTGCAATACAAGATACAAGAAAAGAACAAAAGAAGGGTACAAGTGTCAATATCCAT...

CDS

Download CDS FASTA

1860 bp · LXL04_012085|LXL04_012085|OH1004|CDS

ATGCCAGGCATACCTTTAGTTTCTCGTGAAGTCAATTACTCCAGAGACTCGGATCAGATGTGTCGCCAAGAACCTCGTGTTCTTTTGTCTCCGGAAGAGCAAATTGCAGCTGAAGAAACCCTTTCAGTTTACTGCAAGCCTGTTGAACTCTACAACATTCTTCAACGCCGTGCTATCAAAAGTCCATTGTTTATTCAAAGATGTTTGCAATACAAGATACAAGAAAAGAACAAAAGAAGGGTACAAGTGTCAATATCCAT...

Protein

Download Protein FASTA

619 aa · LXL04_012085|LXL04_012085|OH1004|PROTEIN

MPGIPLVSREVNYSRDSDQMCRQEPRVLLSPEEQIAAEETLSVYCKPVELYNILQRRAIKSPLFIQRCLQYKIQEKNKRRVQVSISISGAFGDKLQTQNLFPLYILLARPFSTPNGERSIVYHFKRARKITAFNGSPKKSLSQAKFIMPEINKLSTEVKSGSLSMLLVSCADITNPKEIDLTKGHIFSSSSNIGGYCLMGKIPLDFLHLSWEKSPNLSLGERVEVMSTVSMQSCFMKLTGTSAKEKCLSFQLPYNSEAVS...

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_012085`
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_012085

Location Chr03:6118942-6122606 (-)

Description Similar to EMF2: Polycomb group protein EMBRYONIC FLOWER 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q8L6Y4`	Polycomb group (PcG) protein.	No verified direct reference in this release
`At4g16845`	Polycomb group (PcG) protein.	The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis.2001 · DOI: 10.1016/s0092-8674(01)00573-6 A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization.2008 · DOI: 10.1073/pnas.0808687105
`UniProt: P0DKJ7`	Polycomb group (PcG) protein.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0306800`	Polycomb group (PcG) protein.	Expression, imprinting, and evolution of rice homologs of the polycomb group genes.2009 · DOI: 10.1093/mp/ssp036
`Os04g0162100`	Polycomb group (PcG) protein.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012085 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009908 flower development Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010048 vernalization response Biological Process

GO:0030154 cell differentiation Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0048586 regulation of long-day photoperiodism, flowering Biological Process

GO:0141044 epigenetic programming in the endosperm Biological Process

GO:0005634 nucleus Cellular Component

GO:0005677 chromatin silencing complex Cellular Component

KEGG gene cross-reference

ath:AT4G16845

ath:AT5G51230

dosa:Os04g0162100

dosa:Os09g0306800

osa:4335036

osa:4346674

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.

Nucleus0.861

Rank 1 · LXL04_012085 · OH-1004

Cytoplasm0.202

Rank 2 · LXL04_012085 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_012085 · OH-1004

Mitochondrion0.029

Rank 4 · LXL04_012085 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_012085 · 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.

PF24663.2DUF765170-277 aa

PF23320.2Zn_SUZ12304-371 aa

PF09733.15VEFS-Box475-597 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012085	`PF24663.2`	DUF7651	70	277	1.8e-82	276.5
LXL04_012085	`PF23320.2`	Zn_SUZ12	304	371	1.1e-31	109.0
LXL04_012085	`PF09733.15`	VEFS-Box	475	597	1.3e-52	177.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8L6Y4`	Arabidopsis thaliana	Polycomb group protein EMBRYONIC FLOWER 2	54.646%	Swiss-Prot	strong database homology
`Q8W5B1`	Arabidopsis thaliana	Polycomb group protein VERNALIZATION 2	50.153%	Swiss-Prot	weak database homology
`P0DKJ7`	Arabidopsis thaliana	Polycomb group protein FERTILIZATION-INDEPENDENT SEED 2	45.946%	Swiss-Prot	weak database homology
`Q69KN0`	Oryza sativa subsp. japonica	Polycomb group protein EMF2B	49.581%	Swiss-Prot	moderate database homology
`Q0JF48`	Oryza sativa subsp. japonica	Polycomb group protein EMF2A	43.429%	Swiss-Prot	moderate database homology

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