LXL04_012593 | RubberDandelionOmics

Gene overview

LXL04_012593

Reference: OH-1004 Chr: Chr03 Coordinates: 15247005-15251618 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1476 bp · LXL04_012593|LXL04_012593|OH1004|cDNA

ATGGCTCCTACTCTCTCTTCTAACACCTACATTCTATTCTTTTGCCTCTTAACATCTCTCTTCTCTGTCATTAGAGCTACTTATAACCTCACACTCCCTCATCAACACCCTAATCCTGAAGCTGTTGTTCAAGAAGTACAAAGGAGATTAAATGTGTCGATTTACAGAAGGGAAATGCTGGACGCCAACAACGGCTGTCTCACCGGAAACCCAATCGACGATTGCTGGCGTTGCGACTCGAACTGGGCGAAAAACCGCGA...

CDS

Download CDS FASTA

1476 bp · LXL04_012593|LXL04_012593|OH1004|CDS

ATGGCTCCTACTCTCTCTTCTAACACCTACATTCTATTCTTTTGCCTCTTAACATCTCTCTTCTCTGTCATTAGAGCTACTTATAACCTCACACTCCCTCATCAACACCCTAATCCTGAAGCTGTTGTTCAAGAAGTACAAAGGAGATTAAATGTGTCGATTTACAGAAGGGAAATGCTGGACGCCAACAACGGCTGTCTCACCGGAAACCCAATCGACGATTGCTGGCGTTGCGACTCGAACTGGGCGAAAAACCGCGA...

Protein

Download Protein FASTA

491 aa · LXL04_012593|LXL04_012593|OH1004|PROTEIN

MAPTLSSNTYILFFCLLTSLFSVIRATYNLTLPHQHPNPEAVVQEVQRRLNVSIYRREMLDANNGCLTGNPIDDCWRCDSNWAKNRERLADCAIGFGKSAVGGKGGQIYVVTDSSDHDVVSPTPGTLRYGVLQTEPLWIVFASSMVIKLKHELIVNSYKTIDGRGANVDITGGGCITLQYVSNVIIHNIRVYDCKPSGNTNIRSSPTHVGYRGRSDGDGISIAGSRNLWIDHCSLSHCTDGLIDAVLGSTAITISNSYFT...

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_012593`
TK1151 ID	TkA02G551190
OH-1004 ID	LXL04_012593
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 95.519 / OH-1004 95.519 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_012593

Location Chr03:15247005-15251618 (-)

Description Similar to At3g53190: Probable pectate lyase 12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g53190`	Probable pectate lyase 12.	No verified direct reference in this release
`At3g54920`	Susceptibility factor required for infection by most powdery mildews, but not by unrelated pathogens.	PMR6, a pectate lyase-like gene required for powdery mildew susceptibility in Arabidopsis.2002 · DOI: 10.1105/tpc.003509
`At4g13710`	Probable pectate lyase 15.	No verified direct reference in this release
`At1g67750`	Probable pectate lyase 5.	No verified direct reference in this release
`At5g63180`	Probable pectate lyase 22.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012593 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009664 plant-type cell wall organization Biological Process

GO:0042547 cell wall modification involved in multidimensional cell growth Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009536 plastid Cellular Component

GO:0016020 membrane Cellular Component

GO:0098552 side of membrane Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G67750

ath:AT3G53190

ath:AT3G54920

ath:AT4G13710

ath:AT5G63180

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.

Lysosome / Vacuole0.265

Rank 1 · LXL04_012593 · OH-1004

Extracellular0.264

Rank 2 · LXL04_012593 · OH-1004

Cell membrane0.195

Rank 3 · LXL04_012593 · OH-1004

Cytoplasm0.148

Rank 4 · LXL04_012593 · OH-1004

Endoplasmic reticulum0.139

Rank 5 · LXL04_012593 · 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.

PF00544.26Pectate_lyase_4150-409 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012593	`PF00544.26`	Pectate_lyase_4	150	409	2.5e-23	83.4

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9SCP2`	Arabidopsis thaliana	Probable pectate lyase 12	59.796%	Swiss-Prot	strong database homology
`Q93Z04`	Arabidopsis thaliana	Probable pectate lyase 13	66.667%	Swiss-Prot	strong database homology
`Q944R1`	Arabidopsis thaliana	Probable pectate lyase 15	61.702%	Swiss-Prot	strong database homology
`Q9FXD8`	Arabidopsis thaliana	Probable pectate lyase 5	64.247%	Swiss-Prot	strong database homology
`Q93Z25`	Arabidopsis thaliana	Probable pectate lyase 22	59.113%	Swiss-Prot	strong database homology

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