LXL04_009243 | RubberDandelionOmics

Gene overview

LXL04_009243

Reference: OH-1004 Chr: Chr02 Coordinates: 121259554-121263031 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1083 bp · LXL04_009243|LXL04_009243|OH1004|cDNA

ATGGCGAAGATATCACAGAAGAGGAGTGCGTCGTCGTCAACTGGAGACAATGCATCCATTGATACAAAGCCGGTGATTAGCAAGGTTAAGAGAACGCGTAAGACGGTTCAGAGAGACTCCCCTCCGCAACGTAGCTCGGTTTACAGAGGCGTCACTAGGCATCGATGGACTGGTCGATATGAAGCTCATTTGTGGGATAAGAATTGTTGGAATGAATCTCAAAACAAAAAAGGACGACAAGGGGCCTACGACGATGAAAA...

CDS

Download CDS FASTA

1083 bp · LXL04_009243|LXL04_009243|OH1004|CDS

ATGGCGAAGATATCACAGAAGAGGAGTGCGTCGTCGTCAACTGGAGACAATGCATCCATTGATACAAAGCCGGTGATTAGCAAGGTTAAGAGAACGCGTAAGACGGTTCAGAGAGACTCCCCTCCGCAACGTAGCTCGGTTTACAGAGGCGTCACTAGGCATCGATGGACTGGTCGATATGAAGCTCATTTGTGGGATAAGAATTGTTGGAATGAATCTCAAAACAAAAAAGGACGACAAGGGGCCTACGACGATGAAAA...

Protein

Download Protein FASTA

360 aa · LXL04_009243|LXL04_009243|OH1004|PROTEIN

MAKISQKRSASSSTGDNASIDTKPVISKVKRTRKTVQRDSPPQRSSVYRGVTRHRWTGRYEAHLWDKNCWNESQNKKGRQGAYDDEKAAAHAYDLAALKYWGQDTILNFPLQTYEEELREMDSLSKEEYIGSLRRKSSGFSRGVSKYRGVARHHHNGRWEARIGRVFGNKYLYLGTFATQEEAATAYDMAAIEYRGLNAVTNFDLSRYIKWLRPNQTDPNNSNGSQPNFDLNPLPDASQDTGLTCCYNNNQNQQPETSSS...

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_009243`
TK1151 ID	TkA03G412690
OH-1004 ID	LXL04_009243
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.200
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_009243

Location Chr02:121259554-121263031 (+)

Description Similar to At1g16060: AP2-like ethylene-responsive transcription factor At1g16060

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g16060`	Probably acts as a transcriptional activator.	No verified direct reference in this release
`At1g79700`	Probably acts as a transcriptional activator.	No verified direct reference in this release
`At3g54320`	May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity).	Contrapuntal networks of gene expression during Arabidopsis seed filling.2002 · DOI: 10.1105/tpc.000877 WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02235.x ACTIVATOR of Spomin::LUC1/WRINKLED1 of Arabidopsis thaliana transactivates sugar-inducible promoters.2005 · DOI: 10.1093/pcp/pci072 A spatiotemporal analysis of enzymatic activities associated with carbon metabolism in wild-type and mutant embryos of Arabidopsis using in situ histochemistry.2006 · DOI: 10.1111/j.1365-313x.2006.02682.x WRI1 is required for seed germination and seedling establishment.2006 · DOI: 10.1104/pp.106.079574 wrinkled1: A novel, low-seed-oil mutant of Arabidopsis with a deficiency in the seed-specific regulation of carbohydrate metabolism.1998 · DOI: 10.1104/pp.118.1.91
`At5g17430`	Transcription factor that, in opposition to HDG1, promotes cell proliferation and morphogenesis via transcriptional activation of meristem and cell proliferation genes, but prevents differentiation, especially during embryogenesis.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0124700`	Acts as a positive regulator of adventitious (crown) root formation by promoting its initiation.	The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling.2011 · DOI: 10.1111/j.1365-313x.2011.04610.x

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009243 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006109 regulation of carbohydrate metabolic process Biological Process

GO:0006110 regulation of glycolytic process Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006629 lipid metabolic process Biological Process

GO:0008610 lipid biosynthetic process Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009744 response to sucrose Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0010187 negative regulation of seed germination Biological Process

KEGG gene cross-reference

ath:AT1G16060

ath:AT1G79700

ath:AT3G54320

dosa:Os07g0124700

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.946

Rank 1 · LXL04_009243 · OH-1004

Cytoplasm0.104

Rank 2 · LXL04_009243 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_009243 · OH-1004

Plastid0.021

Rank 4 · LXL04_009243 · OH-1004

Endoplasmic reticulum0.019

Rank 5 · LXL04_009243 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00847.27AP246-102 aa

PF00847.27AP2145-196 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009243	`PF00847.27`	AP2	46	102	3.7e-19	69.5
LXL04_009243	`PF00847.27`	AP2	145	196	3.7e-19	69.5

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
`Q94AN4`	Arabidopsis thaliana	AP2-like ethylene-responsive transcription factor At1g16060	56.131%	Swiss-Prot	strong database homology
`A0JPZ8`	Arabidopsis thaliana	AP2-like ethylene-responsive transcription factor At1g79700	54.354%	Swiss-Prot	strong database homology
`Q6X5Y6`	Arabidopsis thaliana	Ethylene-responsive transcription factor WRI1	71.782%	Swiss-Prot	moderate database homology
`Q6PQQ4`	Arabidopsis thaliana	AP2-like ethylene-responsive transcription factor BBM	59.276%	Swiss-Prot	moderate database homology
`Q84Z02`	Oryza sativa subsp. japonica	AP2-like ethylene-responsive transcription factor CRL5	69.886%	Swiss-Prot	weak database homology

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