LXL04_001925 | RubberDandelionOmics

Gene overview

LXL04_001925

Reference: OH-1004 Chr: Chr01 Coordinates: 36973672-36975537 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1251 bp · LXL04_001925|LXL04_001925|OH1004|cDNA

ATGACAAATTTACCCTCCCCCGAGGACCGCCGGAACCACTACCTCATCCCGGCTGCCCTCGCATCACTTCTTTTCCTTGGGTCCCTACGCATTTTCTTGGACACTTTCAAAAATAGCCACCAAACATGCCCCTTTTTCCGCCCACAGAGTGGCGGCTACCGTGTCATCAGACCGCCCATTCGTGTTTCAGATGAAGAAACCATAAAAGACGGATGCAATATTTTTGAAGGGAAATGGGTACAGGCAAACGGGTCGTACCC...

CDS

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1251 bp · LXL04_001925|LXL04_001925|OH1004|CDS

ATGACAAATTTACCCTCCCCCGAGGACCGCCGGAACCACTACCTCATCCCGGCTGCCCTCGCATCACTTCTTTTCCTTGGGTCCCTACGCATTTTCTTGGACACTTTCAAAAATAGCCACCAAACATGCCCCTTTTTCCGCCCACAGAGTGGCGGCTACCGTGTCATCAGACCGCCCATTCGTGTTTCAGATGAAGAAACCATAAAAGACGGATGCAATATTTTTGAAGGGAAATGGGTACAGGCAAACGGGTCGTACCC...

Protein

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416 aa · LXL04_001925|LXL04_001925|OH1004|PROTEIN

MTNLPSPEDRRNHYLIPAALASLLFLGSLRIFLDTFKNSHQTCPFFRPQSGGYRVIRPPIRVSDEETIKDGCNIFEGKWVQANGSYPLYTEESCPLLVKQVTCQKNGRPDSSYQKWKWQPDGCNLPRFNALKLLEILRDKRLMFVGDSVQRSMFDSMVCLVQSVITEGKKSLRKQPPRKIFRAEEYNASIEFYWAPFLVESISDHATKHTVLKRLVRLDSISNHSKQWEGVDLLVFESYVWWMYKPVINATYGDLKHVQE...

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_001925`
TK1151 ID	TkA01G498280
OH-1004 ID	LXL04_001925
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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_001925

Location Chr01:36973672-36975537 (-)

Description Similar to TBL31: Protein trichome birefringence-like 31

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g73140`	May act as a bridging protein that binds pectin and other cell wall polysaccharides.	No verified direct reference in this release
`At5g01360`	Involved in secondary cell wall cellulose deposition.	TRICHOME BIREFRINGENCE and its homolog AT5G01360 encode plant-specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis.2010 · DOI: 10.1104/pp.110.153320
`At3g55990`	Xylan acetyltransferase required for 2-O- and 3-O-monoacetylation of xylosyl residues in xylan.	Arabidopsis ESK1 encodes a novel regulator of freezing tolerance.2007 · DOI: 10.1111/j.1365-313x.2006.02994.x Metabolome and water status phenotyping of Arabidopsis under abiotic stress cues reveals new insight into ESK1 function.2009 · DOI: 10.1111/j.1365-3040.2008.01898.x ESKIMO1 is a key gene involved in water economy as well as cold acclimation and salt tolerance.2008 · DOI: 10.1186/1471-2229-8-125 ESKIMO1 disruption in Arabidopsis alters vascular tissue and impairs water transport.2011 · DOI: 10.1371/journal.pone.0016645 The Arabidopsis DUF231 domain-containing protein ESK1 mediates 2-O- and 3-O-acetylation of xylosyl residues in xylan.2013 · DOI: 10.1093/pcp/pct070 Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis Xylan O-acetyltransferase XOAT1.2020 · DOI: 10.1105/tpc.20.00028
`At2g40150`	May act as a bridging protein that binds pectin and other cell wall polysaccharides.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0354400`	Xylan acetyltransferase required for 2-O- and 3-O-monoacetylation of xylosyl residues in xylan.	Biochemical characterization of rice xylan O-acetyltransferases.2018 · DOI: 10.1007/s00425-018-2882-1

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001925 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009409 response to cold Biological Process

GO:0009827 plant-type cell wall modification Biological Process

GO:0030244 cellulose biosynthetic process Biological Process

GO:0045489 pectin biosynthetic process Biological Process

GO:0045492 xylan biosynthetic process Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0050826 response to freezing Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT1G73140

ath:AT2G40150

ath:AT3G55990

ath:AT5G01360

dosa:Os05g0354400

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.

Golgi apparatus0.601

Rank 1 · LXL04_001925 · OH-1004

Cell membrane0.093

Rank 2 · LXL04_001925 · OH-1004

Extracellular0.068

Rank 3 · LXL04_001925 · OH-1004

Endoplasmic reticulum0.062

Rank 4 · LXL04_001925 · OH-1004

Cytoplasm0.032

Rank 5 · LXL04_001925 · 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.

PF14416.12PMR5N71-124 aa

PF13839.13PC-Esterase125-406 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001925	`PF14416.12`	PMR5N	71	124	3.6e-23	82.3
LXL04_001925	`PF13839.13`	PC-Esterase	125	406	2.4e-89	300.8

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
`Q1PFD9`	Arabidopsis thaliana	Protein trichome birefringence-like 31	70.959%	Swiss-Prot	strong database homology
`Q8LED3`	Arabidopsis thaliana	Protein trichome birefringence-like 3	48.397%	Swiss-Prot	moderate database homology
`Q9LY46`	Arabidopsis thaliana	Xylan O-acetyltransferase 1	48.179%	Swiss-Prot	moderate database homology
`Q94K00`	Arabidopsis thaliana	Protein trichome birefringence-like 28	47.527%	Swiss-Prot	moderate database homology
`A0A0P0WL81`	Oryza sativa subsp. japonica	Xylan O-acetyltransferase 5	47.851%	Swiss-Prot	moderate database homology

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