LXL04_027651 | RubberDandelionOmics

Gene overview

LXL04_027651

Reference: OH-1004 Chr: Chr06 Coordinates: 21042340-21047435 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1176 bp · LXL04_027651|LXL04_027651|OH1004|cDNA

ATGGCTTCACACTCAGCAACAACCAAATCGTTAACACTATTCTGCCTTCTCTTCTCTCATTTCGTTGCTGTTTTTACAGCAGAAGACGGCTTACTAATAAACGGCGACTTCGAGACACCGCCATCGGGAGGTTTCGCCGACGAAGGACTCGGCGACAACCCCAACGCAATTCCGAGCTGGAAAGTCAACGGCACAGTGGAACTAGTCGCCTCCGGTCAAAAACAAGGCGGAATGATCCTAATCGTACCAGAAGGTAGACA...

CDS

Download CDS FASTA

1176 bp · LXL04_027651|LXL04_027651|OH1004|CDS

ATGGCTTCACACTCAGCAACAACCAAATCGTTAACACTATTCTGCCTTCTCTTCTCTCATTTCGTTGCTGTTTTTACAGCAGAAGACGGCTTACTAATAAACGGCGACTTCGAGACACCGCCATCGGGAGGTTTCGCCGACGAAGGACTCGGCGACAACCCCAACGCAATTCCGAGCTGGAAAGTCAACGGCACAGTGGAACTAGTCGCCTCCGGTCAAAAACAAGGCGGAATGATCCTAATCGTACCAGAAGGTAGACA...

Protein

Download Protein FASTA

391 aa · LXL04_027651|LXL04_027651|OH1004|PROTEIN

MASHSATTKSLTLFCLLFSHFVAVFTAEDGLLINGDFETPPSGGFADEGLGDNPNAIPSWKVNGTVELVASGQKQGGMILIVPEGRHAVRLGNDAQITQELKLEKGEIYSITFSASRTCAQLESLNVSVPPASQTIDLQTLYSVQGWDTYAWAFQADEEDTHVAFTNPGMEDDPTCGPIIDDIAIKKLFQPTKPKDNAVLNGDFEEGPWMFRNASLGVLLPTNLDEEISSLPGWIVESNRAVRYIDANHFSVPGGKRALE...

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_027651`
TK1151 ID	TkA07G083100
OH-1004 ID	LXL04_027651
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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_027651

Location Chr06:21042340-21047435 (+)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g32460`	May positively regulate PME3 activity in cell-wall pectin modification and associated development.	BIIDXI, the At4g32460 DUF642 gene, is involved in pectin methyl esterase regulation during Arabidopsis thaliana seed germination and plant development.2014 · DOI: 10.1186/s12870-014-0338-8 Cell Wall Localization of Two DUF642 Proteins, BIIDXI and TEEBE, during Meloidogyne incognita Early Inoculation.2017 · DOI: 10.5423/ppj.nt.05.2017.0101
`At5g11420`	Together with BIIDXI, acts as a positive regulator of PME3 activity during several developmental processes, including seed germination and endosperm (testa) rupture at the micropyle, probably by modulating the pectin status in cell walls.	BIIDXI, the At4g32460 DUF642 gene, is involved in pectin methyl esterase regulation during Arabidopsis thaliana seed germination and plant development.2014 · DOI: 10.1186/s12870-014-0338-8
`At5g25460`	Involved in the regulation of testa rupture during seed germination.	Analysis of two L-Galactono-1,4-lactone-responsive genes with complementary expression during the development of Arabidopsis thaliana.2012 · DOI: 10.1093/pcp/pcs014
`At1g80240`	Protein DUF642 L-GALACTONO-1,4-LACTONE-RESPONSIVE GENE 1.	No verified direct reference in this release
`At2g41800`	Prevents hypocotyl epidermal cells elongation by modulating the pectin status in cell walls.	Cell Wall Localization of Two DUF642 Proteins, BIIDXI and TEEBE, during Meloidogyne incognita Early Inoculation.2017 · DOI: 10.5423/ppj.nt.05.2017.0101

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027651 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009624 response to nematode Biological Process

GO:0009630 gravitropism Biological Process

GO:0009664 plant-type cell wall organization Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009845 seed germination Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0045489 pectin biosynthetic process Biological Process

GO:0048598 embryonic morphogenesis Biological Process

GO:0048608 reproductive structure development Biological Process

KEGG gene cross-reference

ath:AT1G80240

ath:AT2G41800

ath:AT4G32460

ath:AT5G11420

ath:AT5G25460

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.

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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.

Cell membrane0.385

Rank 1 · LXL04_027651 · OH-1004

Extracellular0.272

Rank 2 · LXL04_027651 · OH-1004

Lysosome / Vacuole0.162

Rank 3 · LXL04_027651 · OH-1004

Cytoplasm0.160

Rank 4 · LXL04_027651 · OH-1004

Endoplasmic reticulum0.127

Rank 5 · LXL04_027651 · 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.

PF04862.19DUF64230-186 aa

PF04862.19DUF642199-364 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027651	`PF04862.19`	DUF642	30	186	6.7e-84	280.1
LXL04_027651	`PF04862.19`	DUF642	199	364	6.7e-84	280.1

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
`Q8LAR0`	Arabidopsis thaliana	Protein BIIDXI	49.162%	Swiss-Prot	moderate database homology
`Q9LYE7`	Arabidopsis thaliana	BIIDXI-like protein At5g11420	48.596%	Swiss-Prot	moderate database homology
`Q94F20`	Arabidopsis thaliana	Protein DUF642 L-GALACTONO-1,4-LACTONE-RESPONSIVE GENE 2	49.704%	Swiss-Prot	moderate database homology
`Q9SSB7`	Arabidopsis thaliana	Protein DUF642 L-GALACTONO-1,4-LACTONE-RESPONSIVE GENE 1	46.779%	Swiss-Prot	moderate database homology
`O22940`	Arabidopsis thaliana	Protein TEEBE	43.824%	Swiss-Prot	moderate database homology

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