LXL04_001451 | RubberDandelionOmics

Gene overview

LXL04_001451

Reference: OH-1004 Chr: Chr01 Coordinates: 27111534-27115049 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2907 bp · LXL04_001451|LXL04_001451|OH1004|cDNA

ATGAGAGTTTCCGGTGTCCCTTTCGGGGGCCGACTATGGCCTATAGTCATCGCCTTAACAATATTTGGTGTTGCTAACCTTGTAGCAGTTTCAGCCGATCCTTACGTGTATtcttcaccacctccaccataTGTTTACaaatcaccaccaccacccgtacattcaccaccaccaccttatGAGTACAAGTCTCCACCTCCACCGGTGCattcaccaccaccaccatatATGTACAAATCTCCACCTTCACCAGTGCattc...

CDS

Download CDS FASTA

2907 bp · LXL04_001451|LXL04_001451|OH1004|CDS

ATGAGAGTTTCCGGTGTCCCTTTCGGGGGCCGACTATGGCCTATAGTCATCGCCTTAACAATATTTGGTGTTGCTAACCTTGTAGCAGTTTCAGCCGATCCTTACGTGTATTCTTCACCACCTCCACCATATGTTTACAAATCACCACCACCACCCGTACATTCACCACCACCACCTTATGAGTACAAGTCTCCACCTCCACCGGTGCATTCACCACCACCACCATATATGTACAAATCTCCACCTTCACCAGTGCATTC...

Protein

Download Protein FASTA

968 aa · LXL04_001451|LXL04_001451|OH1004|PROTEIN

MRVSGVPFGGRLWPIVIALTIFGVANLVAVSADPYVYSSPPPPYVYKSPPPPVHSPPPPYEYKSPPPPVHSPPPPYMYKSPPSPVHSPPPPYEYKSPPPPVHSPPPPYMYKSPPPPVHSPPPPYVYKSPPPPVHSPPPPYEYKSPPPPVHSPPPPPPPYMYKSPPPPVHSPPPPYEYKSPPPPVHSPPPPYMYKSPPPPVHSPPPPYEYKSPPPPVHSPPPPYMYKSPPPPVYSPPPPYMYKSPPPPVHSPPPPYMYKSP...

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_001451`
TK1151 ID	TkA01G534000
OH-1004 ID	LXL04_001451
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.200
Protein coverage (%)	TK1151 26.362 / OH-1004 18.492 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_001451

Location Chr01:27111534-27115049 (-)

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_001451 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009664 plant-type cell wall organization Biological Process

GO:0010944 negative regulation of transcription by competitive promoter binding Biological Process

GO:0031571 mitotic G1 DNA damage checkpoint signaling Biological Process

GO:0033629 negative regulation of cell adhesion mediated by integrin Biological Process

GO:0043484 regulation of RNA splicing Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0000785 chromatin Cellular Component

GO:0005615 extracellular space Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005796 Golgi lumen Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT1G21310

hsa:389677

hsa:4582

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.

Extracellular0.814

Rank 1 · LXL04_001451 · OH-1004

Cell membrane0.096

Rank 2 · LXL04_001451 · OH-1004

Endoplasmic reticulum0.076

Rank 3 · LXL04_001451 · OH-1004

Cytoplasm0.042

Rank 4 · LXL04_001451 · OH-1004

Nucleus0.023

Rank 5 · LXL04_001451 · 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_233-68 aa

PF04554.19Extensin_2271-327 aa

PF04554.19Extensin_2589-644 aa

PF04554.19Extensin_2620-676 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001451	`PF04554.19`	Extensin_2	33	68	1.2e-68	227.7
LXL04_001451	`PF04554.19`	Extensin_2	271	327	1.2e-68	227.7
LXL04_001451	`PF04554.19`	Extensin_2	589	644	1.2e-68	227.7
LXL04_001451	`PF04554.19`	Extensin_2	620	676	1.2e-68	227.7

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
`Q9FS16`	Arabidopsis thaliana	Extensin-3	40.089%	Swiss-Prot	weak database homology

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