LXL04_020825 | RubberDandelionOmics

Gene overview

LXL04_020825

Reference: OH-1004 Chr: Chr04 Coordinates: 110440873-110443266 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1342 bp · LXL04_020825|LXL04_020825|OH1004|cDNA

ATGTACCATGTGCCTTTGTATGTACTCTCAGAATTCAGTATTAATAATCTCATTCAGCTCACTTGTTTAGCACATTCTTTTCtcctctttctctctttctctctccaTCTCTCTCTATTCTTCCCAAGGGAAGAACAACATGGCAATGCCCATTTTCCTTCTTCTCACTCTTCTTGCTCCTATCTCCACTTTCTCTTCAAATGTACAAGATCCTAACCTTGTAGTAGAACATTTCCACAGGAGAGTTAATGAATCCAGGA...

CDS

Download CDS FASTA

1203 bp · LXL04_020825|LXL04_020825|OH1004|CDS

ATGGCAATGCCCATTTTCCTTCTTCTCACTCTTCTTGCTCCTATCTCCACTTTCTCTTCAAATGTACAAGATCCTAACCTTGTAGTAGAACATTTCCACAGGAGAGTTAATGAATCCAGGAGGAATATGGGATTCTTGTCTTGTGGGACAGGAAATCCAATTGATGATTGTTGGCGATGTGACAAGAATTGGGAACGTAACCGCCAACGTTTAGCAGATTGCGCAATTGGGTTTGGAAAGCAAGCCATTGGTGGTCGTGA...

Protein

Download Protein FASTA

400 aa · LXL04_020825|LXL04_020825|OH1004|PROTEIN

MAMPIFLLLTLLAPISTFSSNVQDPNLVVEHFHRRVNESRRNMGFLSCGTGNPIDDCWRCDKNWERNRQRLADCAIGFGKQAIGGRDGKIYVVTDSKNDDPVNPKPGTLRYGVIQNEPLWIIFAHDMTIKLKEELMMNSFKTIDGRGADVHIAGGPCITIQYVTNIIIHGINIHDCKQGGNTDVRDSPDHSGFRTISDGDGISIFGGSHVWVDHCSLANCHDGLIDAIHGSTAITISNNYMTHHDKVMLLGHSDSSTQDK...

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_020825`
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_020825

Location Chr04:110440873-110443266 (-)

Description Similar to At5g63180: Probable pectate lyase 22

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g63180`	Probable pectate lyase 22.	No verified direct reference in this release
`At1g67750`	Probable pectate lyase 5.	No verified direct reference in this release
`At4g24780`	Probable pectate lyase 18.	No verified direct reference in this release
`At3g27400`	Putative pectate lyase 11.	No verified direct reference in this release
`At4g13710`	Probable pectate lyase 15.	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_020825 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009624 response to nematode Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G67750

ath:AT3G27400

ath:AT4G13710

ath:AT4G24780

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.

Extracellular0.504

Rank 1 · LXL04_020825 · OH-1004

Lysosome / Vacuole0.215

Rank 2 · LXL04_020825 · OH-1004

Cytoplasm0.109

Rank 3 · LXL04_020825 · OH-1004

Endoplasmic reticulum0.090

Rank 4 · LXL04_020825 · OH-1004

Cell membrane0.071

Rank 5 · LXL04_020825 · 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_4132-335 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_020825	`PF00544.26`	Pectate_lyase_4	132	335	8e-23	81.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q93Z25`	Arabidopsis thaliana	Probable pectate lyase 22	77.250%	Swiss-Prot	strong database homology
`Q9FXD8`	Arabidopsis thaliana	Probable pectate lyase 5	79.328%	Swiss-Prot	strong database homology
`Q9C5M8`	Arabidopsis thaliana	Probable pectate lyase 18	77.215%	Swiss-Prot	strong database homology
`Q9LTZ0`	Arabidopsis thaliana	Putative pectate lyase 11	74.257%	Swiss-Prot	strong database homology
`Q944R1`	Arabidopsis thaliana	Probable pectate lyase 15	69.974%	Swiss-Prot	strong database homology

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