LXL04_010080 | RubberDandelionOmics

Gene overview

LXL04_010080

Reference: OH-1004 Chr: Chr02 Coordinates: 139510060-139513686 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2181 bp · LXL04_010080|LXL04_010080|OH1004|cDNA

ATGTTTCAACCGAACATGTTTGAGAGTCATCATCATATTCTTGATATGAGCCATAAAACCCAAGAAAATGAGCTCGATATGCTAAGAGATGAGGAATTCGAGAGCAAATCCGGCACTGATATCATGGAAGCTCACTCCGGTGATGATCAAGATCCTAATCAACGACCCAACAAAAAGAAACGATACCATCGTCACACCCAACATCAAATCCAAGAAATGGAATCGTTTTTCAAAGAATGCCCACATCCAGATGATAAGCA...

CDS

Download CDS FASTA

2181 bp · LXL04_010080|LXL04_010080|OH1004|CDS

ATGTTTCAACCGAACATGTTTGAGAGTCATCATCATATTCTTGATATGAGCCATAAAACCCAAGAAAATGAGCTCGATATGCTAAGAGATGAGGAATTCGAGAGCAAATCCGGCACTGATATCATGGAAGCTCACTCCGGTGATGATCAAGATCCTAATCAACGACCCAACAAAAAGAAACGATACCATCGTCACACCCAACATCAAATCCAAGAAATGGAATCGTTTTTCAAAGAATGCCCACATCCAGATGATAAGCA...

Protein

Download Protein FASTA

726 aa · LXL04_010080|LXL04_010080|OH1004|PROTEIN

MFQPNMFESHHHILDMSHKTQENELDMLRDEEFESKSGTDIMEAHSGDDQDPNQRPNKKKRYHRHTQHQIQEMESFFKECPHPDDKQRKELGRRLTLEPLQVKFWFQNKRTQMKAQHERHENTQLRNENDKLRSENIRYKEALANATCPNCGGPAAIGEMSFDEQHLRIENARLREEIDRISGIAAKYVGKPMLSYPNLSPHGPTRSLDLGVASFSPQQGMVGDMFGANDLLRSVSGPTEADKPIIIELAVAAMEELIRM...

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_010080`
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_010080

Location Chr02:139510060-139513686 (-)

Description Similar to PDF2: Homeobox-leucine zipper protein PROTODERMAL FACTOR 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g04890`	Probable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'.	Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis.2003 · DOI: 10.1242/dev.00292 Mutations in epidermis-specific HD-ZIP IV genes affect floral organ identity in Arabidopsis thaliana.2013 · DOI: 10.1111/tpj.12211 Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element.2014 · DOI: 10.1105/tpc.114.127647
`At4g21750`	Probable transcription factor involved in cell specification and pattern formation during embryogenesis.	Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein.2001 · DOI: 10.1046/j.1365-313x.2001.01047.x Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis.2003 · DOI: 10.1242/dev.00292 Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element.2014 · DOI: 10.1105/tpc.114.127647
`At1g05230`	Probable transcription factor (By similarity).	Mutations in epidermis-specific HD-ZIP IV genes affect floral organ identity in Arabidopsis thaliana.2013 · DOI: 10.1111/tpj.12211

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0627000`	Probable transcription factor.	No verified direct reference in this release
`Os08g0187500`	Probable transcription factor that may be involved in protoderm differentiation and radial pattern formation during early embryogenesis.	Position dependent expression of GL2-type homeobox gene, Roc1: significance for protoderm differentiation and radial pattern formation in early rice embryogenesis.2002 · DOI: 10.1046/j.1365-313x.2002.01234.x

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010080 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009845 seed germination Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0010090 trichome morphogenesis Biological Process

GO:0010214 seed coat development Biological Process

GO:0030154 cell differentiation Biological Process

GO:0048354 mucilage biosynthetic process involved in seed coat development Biological Process

GO:0048497 maintenance of floral organ identity Biological Process

GO:0048825 cotyledon development Biological Process

GO:0052541 plant-type cell wall cellulose metabolic process Biological Process

GO:0090627 plant epidermal cell differentiation Biological Process

GO:2000033 regulation of seed dormancy process Biological Process

KEGG gene cross-reference

ath:AT1G05230

ath:AT4G04890

ath:AT4G21750

dosa:Os04g0627000

dosa:Os08g0187500

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.

Nucleus0.892

Rank 1 · LXL04_010080 · OH-1004

Cytoplasm0.143

Rank 2 · LXL04_010080 · OH-1004

Cell membrane0.059

Rank 3 · LXL04_010080 · OH-1004

Endoplasmic reticulum0.027

Rank 4 · LXL04_010080 · OH-1004

Plastid0.023

Rank 5 · LXL04_010080 · 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.

PF00046.36Homeodomain59-114 aa

PF01852.26START249-468 aa

PF25797.2PDF2_C487-723 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010080	`PF00046.36`	Homeodomain	59	114	3.4e-17	62.7
LXL04_010080	`PF01852.26`	START	249	468	4e-55	187.1
LXL04_010080	`PF25797.2`	PDF2_C	487	723	6.3e-100	333.9

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
`Q93V99`	Arabidopsis thaliana	Homeobox-leucine zipper protein PROTODERMAL FACTOR 2	79.973%	Swiss-Prot	strong database homology
`Q8RWU4`	Arabidopsis thaliana	Homeobox-leucine zipper protein MERISTEM L1	77.836%	Swiss-Prot	strong database homology
`Q94C37`	Arabidopsis thaliana	Homeobox-leucine zipper protein HDG2	73.098%	Swiss-Prot	strong database homology
`Q0J9X2`	Oryza sativa subsp. japonica	Homeobox-leucine zipper protein ROC2	77.980%	Swiss-Prot	strong database homology
`Q6ZAR0`	Oryza sativa subsp. japonica	Homeobox-leucine zipper protein ROC1	77.479%	Swiss-Prot	strong database homology

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