LXL04_033309 | RubberDandelionOmics

Gene overview

LXL04_033309

Reference: OH-1004 Chr: Chr07 Coordinates: 40652333-40655929 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1350 bp · LXL04_033309|LXL04_033309|OH1004|cDNA

ATGACAATGGAGGTACCTAAGAAGTGGTTCGCTATATGTTCCTTTCTGTTTCTGATGCTCTTGCTTGCCACCATCGCCGCCGTCGTGCAGAAAAACGACTCCTCAAACTCCAGGACTGTGGAAGCAGAGCAATTGCAGAGCCGGAACTTCAACTCATCAATGGCGGCAAGAGAAAAGGAGATGGAAGCTTTGAATGAAAATGCCGTTCAAGATCCAGAAGAAGTCATTTCCCTTCTTGAAATGACAATGAGAAACAACAC...

CDS

Download CDS FASTA

1350 bp · LXL04_033309|LXL04_033309|OH1004|CDS

ATGACAATGGAGGTACCTAAGAAGTGGTTCGCTATATGTTCCTTTCTGTTTCTGATGCTCTTGCTTGCCACCATCGCCGCCGTCGTGCAGAAAAACGACTCCTCAAACTCCAGGACTGTGGAAGCAGAGCAATTGCAGAGCCGGAACTTCAACTCATCAATGGCGGCAAGAGAAAAGGAGATGGAAGCTTTGAATGAAAATGCCGTTCAAGATCCAGAAGAAGTCATTTCCCTTCTTGAAATGACAATGAGAAACAACAC...

Protein

Download Protein FASTA

449 aa · LXL04_033309|LXL04_033309|OH1004|PROTEIN

MTMEVPKKWFAICSFLFLMLLLATIAAVVQKNDSSNSRTVEAEQLQSRNFNSSMAAREKEMEALNENAVQDPEEVISLLEMTMRNNTERRKLGYFSCGTGNPIDDCWRCDRNWHRNRKRLADCGIGFGRNAIGGRHGRFYVVTDSRDDNPVNPRPGTLRHAVIQTQPLWIIFKRNMVIQLKQELIINSFKTIDGRGVNVHIAYGGCLTLQFITNVIIHGLHIHDCKPTGNALVRSSPSHYGWRTMADGDAISIFGSSHIW...

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_033309`
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_033309

Location Chr07:40652333-40655929 (+)

Description Similar to At4g13710: Probable pectate lyase 15

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g13710`	Probable pectate lyase 15.	No verified direct reference in this release
`At1g04680`	Probable pectate lyase 1.	No verified direct reference in this release
`At3g07010`	Probable pectate lyase 8.	No verified direct reference in this release
`At3g24670`	Probable pectate lyase 10.	No verified direct reference in this release
`At3g24230`	Probable pectate lyase 9.	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_033309 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0045490 pectin catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G04680

ath:AT3G07010

ath:AT3G24230

ath:AT3G24670

ath:AT4G13710

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.

Extracellular0.520

Rank 1 · LXL04_033309 · OH-1004

Lysosome / Vacuole0.169

Rank 2 · LXL04_033309 · OH-1004

Cytoplasm0.130

Rank 3 · LXL04_033309 · OH-1004

Endoplasmic reticulum0.087

Rank 4 · LXL04_033309 · OH-1004

Cell membrane0.077

Rank 5 · LXL04_033309 · 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_4181-384 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033309	`PF00544.26`	Pectate_lyase_4	181	384	6.7e-19	68.8

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
`Q944R1`	Arabidopsis thaliana	Probable pectate lyase 15	75.814%	Swiss-Prot	strong database homology
`Q940Q1`	Arabidopsis thaliana	Probable pectate lyase 1	83.127%	Swiss-Prot	strong database homology
`Q9M8Z8`	Arabidopsis thaliana	Probable pectate lyase 8	79.639%	Swiss-Prot	strong database homology
`Q9LJ42`	Arabidopsis thaliana	Probable pectate lyase 10	71.233%	Swiss-Prot	strong database homology
`Q9LRM5`	Arabidopsis thaliana	Probable pectate lyase 9	68.636%	Swiss-Prot	strong database homology

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