LXL04_021401 | RubberDandelionOmics

Gene overview

LXL04_021401

Reference: OH-1004 Chr: Chr04 Coordinates: 128875049-128876151 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1008 bp · LXL04_021401|LXL04_021401|OH1004|cDNA

ATGGATGGAAGTTCCACAGAAGAACAAAGCACAACTACTGAAACAACTTCAACAGTCGCTGCACCGGTGACTTCGCCGCCACTGATCGGAAGTGGTGGCAGCGTTGTTCTCGACATGGAAGGTGGTTTAGAAGCCGAGTCAAGGAAGTTGCCTTCCTCAAGGTTCAAAGGTGTAGTCCCACAGCCTAACGGCCGTTGGGGTGCTCAGATTTACGAGAAGCACCAACGCGTGTGGCTTGGGACCTTCAACGAAGAACATGA...

CDS

Download CDS FASTA

1008 bp · LXL04_021401|LXL04_021401|OH1004|CDS

ATGGATGGAAGTTCCACAGAAGAACAAAGCACAACTACTGAAACAACTTCAACAGTCGCTGCACCGGTGACTTCGCCGCCACTGATCGGAAGTGGTGGCAGCGTTGTTCTCGACATGGAAGGTGGTTTAGAAGCCGAGTCAAGGAAGTTGCCTTCCTCAAGGTTCAAAGGTGTAGTCCCACAGCCTAACGGCCGTTGGGGTGCTCAGATTTACGAGAAGCACCAACGCGTGTGGCTTGGGACCTTCAACGAAGAACATGA...

Protein

Download Protein FASTA

335 aa · LXL04_021401|LXL04_021401|OH1004|PROTEIN

MDGSSTEEQSTTTETTSTVAAPVTSPPLIGSGGSVVLDMEGGLEAESRKLPSSRFKGVVPQPNGRWGAQIYEKHQRVWLGTFNEEHEAAKAYDTAVQRFRGRDAVTNFKPLPADTEEAGLEASFLNSHSKSEIVDMLRKHTYNDELEQSKRSCSLNKTPFTNGFRSGQHLVNAREQLFEKTVTPSDVGKLNRLVIPKQHAEKHFPLQSGSTSKGVLLHFEDIGMKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDI...

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_021401`
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_021401

Location Chr04:128875049-128876151 (-)

Description Similar to RAV1: AP2/ERF and B3 domain-containing transcription factor RAV1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g13260`	Binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'.	Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development.2004 · DOI: 10.1038/sj.cr.7290197 RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants.1999 · DOI: 10.1093/nar/27.2.470
`At1g25560`	Transcriptional repressor of flowering time on long day plants.	The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering.2008 · DOI: 10.1016/j.cub.2008.07.075
`At1g68840`	Probably acts as a transcriptional activator.	The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering.2008 · DOI: 10.1016/j.cub.2008.07.075
`At3g25730`	Probably acts as a transcriptional activator.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0693400`	AP2/ERF and B3 domain-containing protein Os01g0693400.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021401 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048366 leaf development Biological Process

GO:0048527 lateral root development Biological Process

GO:0048573 photoperiodism, flowering Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G13260

ath:AT1G25560

ath:AT1G68840

ath:AT3G25730

dosa:Os01g0693400

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.

Nucleus0.955

Rank 1 · LXL04_021401 · OH-1004

Cytoplasm0.099

Rank 2 · LXL04_021401 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_021401 · OH-1004

Endoplasmic reticulum0.021

Rank 4 · LXL04_021401 · OH-1004

Plastid0.014

Rank 5 · LXL04_021401 · 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.

PF00847.27AP253-101 aa

PF02362.27B3178-278 aa

PF31239.1At5g26805_C179-264 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021401	`PF00847.27`	AP2	53	101	3.5e-08	34.3
LXL04_021401	`PF02362.27`	B3	178	278	1.2e-26	93.3
LXL04_021401	`PF31239.1`	At5g26805_C	179	264	6e-06	27.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9ZWM9`	Arabidopsis thaliana	AP2/ERF and B3 domain-containing transcription factor RAV1	64.615%	Swiss-Prot	strong database homology
`Q9C6M5`	Arabidopsis thaliana	AP2/ERF and B3 domain-containing transcription repressor TEM1	60.933%	Swiss-Prot	strong database homology
`P82280`	Arabidopsis thaliana	AP2/ERF and B3 domain-containing transcription repressor RAV2	60.000%	Swiss-Prot	strong database homology
`Q9LS06`	Arabidopsis thaliana	AP2/ERF and B3 domain-containing transcription factor ARF14	61.059%	Swiss-Prot	strong database homology
`Q8RZX9`	Oryza sativa subsp. japonica	AP2/ERF and B3 domain-containing protein Os01g0693400	58.154%	Swiss-Prot	strong database homology

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