LXL04_005274 | RubberDandelionOmics

Gene overview

LXL04_005274

Reference: OH-1004 Chr: Chr01 Coordinates: 159533294-159536621 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1212 bp · LXL04_005274|LXL04_005274|OH1004|cDNA

ATGCATATAAACGACCCTATGCTGATCCTATTTTCCACTCCAAAACAATTTTAtcccactctctttctctctctttctctccaaATGCACAGGGTTTCAATTATTGAGGCAGCCACCCTGCTGTCGGCGTTGCTACTGTGCGCCACCGTCCACACCGCCGTTGGAGTTTCCGACGGTTTGTTGTATAATGGAAATTTTGAACTTGGACCGAAGCCTACGGATTTGAAAGGCACGGAGGTGCTAAAGCACGATGCGATTCC...

CDS

Download CDS FASTA

1212 bp · LXL04_005274|LXL04_005274|OH1004|CDS

ATGCATATAAACGACCCTATGCTGATCCTATTTTCCACTCCAAAACAATTTTATCCCACTCTCTTTCTCTCTCTTTCTCTCCAAATGCACAGGGTTTCAATTATTGAGGCAGCCACCCTGCTGTCGGCGTTGCTACTGTGCGCCACCGTCCACACCGCCGTTGGAGTTTCCGACGGTTTGTTGTATAATGGAAATTTTGAACTTGGACCGAAGCCTACGGATTTGAAAGGCACGGAGGTGCTAAAGCACGATGCGATTCC...

Protein

Download Protein FASTA

403 aa · LXL04_005274|LXL04_005274|OH1004|PROTEIN

MHINDPMLILFSTPKQFYPTLFLSLSLQMHRVSIIEAATLLSALLLCATVHTAVGVSDGLLYNGNFELGPKPTDLKGTEVLKHDAIPGWKLFGFVEYIKSGQKQGDMLLVVPEGAYAVRLGNEATIEQTINVTKGMYYSITFSAARTCAQEETLNVSVAPDFGVLPMQTLYSSSGWDSYAWAFQAEYSQVTIKLHNPGVEEDPACGPLIDSIAIKALYPPKPSKENILKNGGFEEGPYIFPNTTWGVLVPPNIEDDHSPL...

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_005274`
TK1151 ID	TkA01G070720
OH-1004 ID	LXL04_005274
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.200
Protein coverage (%)	TK1151 100.000 / OH-1004 93.052 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_005274

Location Chr01:159533294-159536621 (+)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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_005274 · 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.

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.

Extracellular0.371

Rank 1 · LXL04_005274 · OH-1004

Cell membrane0.189

Rank 2 · LXL04_005274 · OH-1004

Lysosome / Vacuole0.154

Rank 3 · LXL04_005274 · OH-1004

Endoplasmic reticulum0.131

Rank 4 · LXL04_005274 · OH-1004

Cytoplasm0.123

Rank 5 · LXL04_005274 · 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.

PF04862.19DUF64259-215 aa

PF04862.19DUF642227-393 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005274	`PF04862.19`	DUF642	59	215	4.8e-89	296.8
LXL04_005274	`PF04862.19`	DUF642	227	393	4.8e-89	296.8

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
`Q9LYE7`	Arabidopsis thaliana	BIIDXI-like protein At5g11420	78.371%	Swiss-Prot	strong database homology
`Q94F20`	Arabidopsis thaliana	Protein DUF642 L-GALACTONO-1,4-LACTONE-RESPONSIVE GENE 2	73.171%	Swiss-Prot	strong database homology
`Q8LAR0`	Arabidopsis thaliana	Protein BIIDXI	72.472%	Swiss-Prot	strong database homology
`Q9SSB7`	Arabidopsis thaliana	Protein DUF642 L-GALACTONO-1,4-LACTONE-RESPONSIVE GENE 1	62.360%	Swiss-Prot	strong database homology
`O22940`	Arabidopsis thaliana	Protein TEEBE	52.941%	Swiss-Prot	strong database homology

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