LXL04_001480 | RubberDandelionOmics

Gene overview

LXL04_001480

Reference: OH-1004 Chr: Chr01 Coordinates: 27432915-27448978 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1995 bp · LXL04_001480|LXL04_001480|OH1004|cDNA

ATGGGGAGAGGGAAGATTGTAATTCGAAGGATCGATAACTCAACCAGCAGGCAAGTTACTTTTTCTAAAAGAAGAAATGGGTTGTTGAAGAAGGCGAAGGAGTTGGCTATTTTGTGCGATGCTGAAGTCGGACTCATTGTCTTCTCTAGCACTGGGAAGCTCCACGAGTTCGCTAGCTCAAGCATGAAAACAGTTACTGAGCGGTACACCAAAGTGAAGGAGGAACATCATCAACTGATGAATACTTCTTCAGAAGCCAA...

CDS

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1995 bp · LXL04_001480|LXL04_001480|OH1004|CDS

ATGGGGAGAGGGAAGATTGTAATTCGAAGGATCGATAACTCAACCAGCAGGCAAGTTACTTTTTCTAAAAGAAGAAATGGGTTGTTGAAGAAGGCGAAGGAGTTGGCTATTTTGTGCGATGCTGAAGTCGGACTCATTGTCTTCTCTAGCACTGGGAAGCTCCACGAGTTCGCTAGCTCAAGCATGAAAACAGTTACTGAGCGGTACACCAAAGTGAAGGAGGAACATCATCAACTGATGAATACTTCTTCAGAAGCCAA...

Protein

Download Protein FASTA

664 aa · LXL04_001480|LXL04_001480|OH1004|PROTEIN

MGRGKIVIRRIDNSTSRQVTFSKRRNGLLKKAKELAILCDAEVGLIVFSSTGKLHEFASSSMKTVTERYTKVKEEHHQLMNTSSEAKKENGGLGVGSLKAMNLALLIKWIWRFKADPSNLWRRVVAGIRNGNNKPIQKSGLKSLKGVWSRIISSLEDLKDTNIDLSDLIRSQVGNGNSTLFWFDHWADKETMASLFPELFELEKHKGCLVADRRIHSNSVASMGRIPTATAISRRGVRVDSSSCPLCISGSDEADHTLIK...

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_001480`
TK1151 ID	TkA01G532370
OH-1004 ID	LXL04_001480
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	97.800
Protein coverage (%)	TK1151 47.849 / OH-1004 13.404 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_001480

Location Chr01:27432915-27448978 (-)

Description Similar to PME26: Putative pectinesterase/pectinesterase inhibitor 26

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14300`	Acts in the modification of cell walls via demethylesterification of cell wall pectin.	No verified direct reference in this release
`At1g53840`	Acts in the modification of cell walls via demethylesterification of cell wall pectin (By similarity).	Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors.2017 · DOI: 10.1111/pce.13038
`At2g14210`	Probable transcription factor.	Nitrate and glutamate sensing by plant roots.2005 · DOI: 10.1042/bst0330283 The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches.2006 · DOI: 10.1073/pnas.0605275103 An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture.1998 · DOI: 10.1126/science.279.5349.407

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0431900`	Probable transcription factor.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001480 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0042545 cell wall modification Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0000325 plant-type vacuole Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005768 endosome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005802 trans-Golgi network Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009506 plasmodesma Cellular Component

KEGG gene cross-reference

ath:AT1G53840

ath:AT3G14300

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.

Cytoplasm0.307

Rank 1 · LXL04_001480 · OH-1004

Nucleus0.253

Rank 2 · LXL04_001480 · OH-1004

Cell membrane0.251

Rank 3 · LXL04_001480 · OH-1004

Endoplasmic reticulum0.140

Rank 4 · LXL04_001480 · OH-1004

Lysosome / Vacuole0.081

Rank 5 · LXL04_001480 · 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.

PF00319.24SRF-TF10-57 aa

PF04043.21PMEI360-416 aa

PF01095.26Pectinesterase459-530 aa

PF01486.23K-box557-639 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001480	`PF00319.24`	SRF-TF	10	57	2.1e-25	88.6
LXL04_001480	`PF04043.21`	PMEI	360	416	4.4e-12	47.1
LXL04_001480	`PF01095.26`	Pectinesterase	459	530	5.1e-19	68.8
LXL04_001480	`PF01486.23`	K-box	557	639	1.7e-20	73.7

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
`Q9LUL8`	Arabidopsis thaliana	Putative pectinesterase/pectinesterase inhibitor 26	51.053%	Swiss-Prot	weak database homology
`Q43867`	Arabidopsis thaliana	Pectinesterase 1	49.741%	Swiss-Prot	weak database homology
`Q9SI38`	Arabidopsis thaliana	MADS-box transcription factor ANR1	80.682%	Swiss-Prot	weak database homology
`Q6VAM4`	Oryza sativa subsp. japonica	MADS-box transcription factor 23	74.713%	Swiss-Prot	weak database homology

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