LXL04_001449 | RubberDandelionOmics

Gene overview

LXL04_001449

Reference: OH-1004 Chr: Chr01 Coordinates: 27080378-27083859 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2814 bp · LXL04_001449|LXL04_001449|OH1004|cDNA

ATGAGAGTTTCCACCGGCAACGGTGTTCCTTTCGGGGGCCGACTATGGCCTTTAGTCATCGCATTAACAATATTTGGTGTTGCTAATCTTATAGCAGTTTCAGCCGATCCTTATGTGTATTCTTCACCTCCTCCACCATATGTTTACAAATCACCACCTCCACCCGTACATTCACCACCACCGCCTTATGAGTACAAGTCCCCACCACCACCATATATGTACAAGTCTCCTCCTCCACCCGTCCATTCACCACCACCACT...

CDS

Download CDS FASTA

2814 bp · LXL04_001449|LXL04_001449|OH1004|CDS

ATGAGAGTTTCCACCGGCAACGGTGTTCCTTTCGGGGGCCGACTATGGCCTTTAGTCATCGCATTAACAATATTTGGTGTTGCTAATCTTATAGCAGTTTCAGCCGATCCTTATGTGTATTCTTCACCTCCTCCACCATATGTTTACAAATCACCACCTCCACCCGTACATTCACCACCACCGCCTTATGAGTACAAGTCCCCACCACCACCATATATGTACAAGTCTCCTCCTCCACCCGTCCATTCACCACCACCACT...

Protein

Download Protein FASTA

937 aa · LXL04_001449|LXL04_001449|OH1004|PROTEIN

MRVSTGNGVPFGGRLWPLVIALTIFGVANLIAVSADPYVYSSPPPPYVYKSPPPPVHSPPPPYEYKSPPPPYMYKSPPPPVHSPPPLYMYKSPPPPVHSPPPPYEYKSPPPPVHSPPPPYMYKSPPPPAHSPPPPYMYKSPPPPVHSPPPPYEYNSPPPPVHSPPPPYMYKSPPPPVHSPPPYLYKSPPPPVHSPPPPPYEYNSPPPPVHSPPPPYMYKSPPPPVHSPPPPYIYKSPPPPVHSPRPYLYKSPPPPVHSPP...

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_001449`
TK1151 ID	TkA01G534330
OH-1004 ID	LXL04_001449
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 13.535 / OH-1004 7.150 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_001449

Location Chr01:27080378-27083859 (-)

Description Similar to EXT3: Extensin-3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g21310`	Structural component which strengthens the primary cell wall.	Characterization of four extensin genes in Arabidopsis thaliana by differential gene expression under stress and non-stress conditions.2001 · DOI: 10.1093/dnares/8.3.115 Self-assembly of the plant cell wall requires an extensin scaffold.2008 · DOI: 10.1073/pnas.0711980105

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001449 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009664 plant-type cell wall organization Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009530 primary cell wall Cellular Component

GO:0016324 apical plasma membrane Cellular Component

GO:0005199 structural constituent of cell wall Molecular Function

KEGG gene cross-reference

ath:AT1G21310

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.

Extracellular0.870

Rank 1 · LXL04_001449 · OH-1004

Cell membrane0.061

Rank 2 · LXL04_001449 · OH-1004

Endoplasmic reticulum0.060

Rank 3 · LXL04_001449 · OH-1004

Cytoplasm0.036

Rank 4 · LXL04_001449 · OH-1004

Nucleus0.014

Rank 5 · LXL04_001449 · 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.

PF04554.19Extensin_236-71 aa

PF04554.19Extensin_247-96 aa

PF04554.19Extensin_272-128 aa

PF04554.19Extensin_2152-208 aa

PF04554.19Extensin_2216-271 aa

PF04554.19Extensin_2565-620 aa

PF04554.19Extensin_2660-708 aa

PF04554.19Extensin_2685-741 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001449	`PF04554.19`	Extensin_2	36	71	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	47	96	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	72	128	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	152	208	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	216	271	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	565	620	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	660	708	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	685	741	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	765	821	1.8e-70	233.6
LXL04_001449	`PF04554.19`	Extensin_2	877	934	1.8e-70	233.6

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
`Q9FS16`	Arabidopsis thaliana	Extensin-3	36.343%	Swiss-Prot	weak database homology

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