LXL04_032725 | RubberDandelionOmics

Gene overview

LXL04_032725

Reference: OH-1004 Chr: Chr07 Coordinates: 28372366-28373878 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1057 bp · LXL04_032725|LXL04_032725|OH1004|cDNA

TGACAATAGGTACGGACTTCCAACATACAAACGTGCCACATATCCATCCAAGGTCAACGTAGGACGCCTACAGAAAATGGCTCCAATTCTCCCCTACGCTCACTGCGAGACCAAATTACGAGCTCTCGCCGGCCAAGCTGAGGGATTCGGCCGCCTTGCCACCGGTGGACTTCATGGACCACTCTACTGTGTCACTACTCTTGCCGATGATGGTCCTGGTTCACTACGTGATGCATGTCGCAAGAAAGAACCTTTATGGA...

CDS

Download CDS FASTA

981 bp · LXL04_032725|LXL04_032725|OH1004|CDS

ATGGCTCCAATTCTCCCCTACGCTCACTGCGAGACCAAATTACGAGCTCTCGCCGGCCAAGCTGAGGGATTCGGCCGCCTTGCCACCGGTGGACTTCATGGACCACTCTACTGTGTCACTACTCTTGCCGATGATGGTCCTGGTTCACTACGTGATGCATGTCGCAAGAAAGAACCTTTATGGATTGTTTTTGAAATATCGGGTGAAATTAAACTGAAATCTATTCTACCCGTGTCTTCATATAAAACAATTGATGGTCG...

Protein

Download Protein FASTA

326 aa · LXL04_032725|LXL04_032725|OH1004|PROTEIN

MAPILPYAHCETKLRALAGQAEGFGRLATGGLHGPLYCVTTLADDGPGSLRDACRKKEPLWIVFEISGEIKLKSILPVSSYKTIDGRGQWIRITGMGLRLDQCEHVIICNLEFQEGRGHDVDAIQIKPNSKHIWIDRCSLKDYSDGLVDVTRGSTDVTISRCKFGYHDKTILIGANAGHCDDRNIRVTIHHCLFDGSRQRLPRVRFAKVHLYNNYTRYWAIYAVGASVESQIYSQCNIYEAGRDCNVAFKYIPEKAGDKN...

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_032725`
TK1151 ID	TkA08G200740
OH-1004 ID	LXL04_032725
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_032725

Location Chr07:28372366-28373878 (+)

Description Similar to At1g30350: Probable pectate lyase 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g30350`	Probable pectate lyase 4.	No verified direct reference in this release
`At5g55720`	Putative pectate lyase 21.	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
`At1g11920`	Putative pectate lyase 2.	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_032725 · 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:0005886 plasma membrane 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:AT1G11920

ath:AT1G30350

ath:AT3G54920

ath:AT5G55720

sly:101253756

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.

Cytoplasm0.466

Rank 1 · LXL04_032725 · OH-1004

Nucleus0.240

Rank 2 · LXL04_032725 · OH-1004

Mitochondrion0.224

Rank 3 · LXL04_032725 · OH-1004

Peroxisome0.117

Rank 4 · LXL04_032725 · OH-1004

Extracellular0.090

Rank 5 · LXL04_032725 · 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_473-258 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032725	`PF00544.26`	Pectate_lyase_4	73	258	3.9e-27	95.9

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
`Q9C8G4`	Arabidopsis thaliana	Probable pectate lyase 4	42.083%	Swiss-Prot	moderate database homology
`Q9FM66`	Arabidopsis thaliana	Putative pectate lyase 21	40.161%	Swiss-Prot	moderate database homology
`Q93Z04`	Arabidopsis thaliana	Probable pectate lyase 13	35.347%	Swiss-Prot	moderate database homology
`O65388`	Arabidopsis thaliana	Putative pectate lyase 2	40.551%	Swiss-Prot	moderate database homology

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