LXL04_025206 | RubberDandelionOmics

Gene overview

LXL04_025206

Reference: OH-1004 Chr: Chr05 Coordinates: 107549903-107551531 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1182 bp · LXL04_025206|LXL04_025206|OH1004|cDNA

ATGGGAAAAGCCTCTTTCATTCTTTCTTTCACCCATGCCTTCGTTTTTATGGTACCGCTTATTTTAGCTAGGACCATACAAGATGAAGGATCCACATTGGGAGCCAATTCAACAAGGAGGGAGCTTCATGGCGGATGCGAAGCTTTtaacaaaatcgacaaatgcTGGAGGTGCAAAGCCGATTGGGCAGAAAACCGTCAAGCATTAGCCGATTGTGCACTTGGATTTGCAAAAGGAACCACCGGCGGCAAGGGCGGCGA...

CDS

Download CDS FASTA

1182 bp · LXL04_025206|LXL04_025206|OH1004|CDS

ATGGGAAAAGCCTCTTTCATTCTTTCTTTCACCCATGCCTTCGTTTTTATGGTACCGCTTATTTTAGCTAGGACCATACAAGATGAAGGATCCACATTGGGAGCCAATTCAACAAGGAGGGAGCTTCATGGCGGATGCGAAGCTTTTAACAAAATCGACAAATGCTGGAGGTGCAAAGCCGATTGGGCAGAAAACCGTCAAGCATTAGCCGATTGTGCACTTGGATTTGCAAAAGGAACCACCGGCGGCAAGGGCGGCGA...

Protein

Download Protein FASTA

393 aa · LXL04_025206|LXL04_025206|OH1004|PROTEIN

MGKASFILSFTHAFVFMVPLILARTIQDEGSTLGANSTRRELHGGCEAFNKIDKCWRCKADWAENRQALADCALGFAKGTTGGKGGEIYEVTDPSDDDAVNPKPGTLRCGVTQDRPLWIIFKKDMVIKLKHELVITSDKTIDGRGACVQIANGAGLTVMKVKNVIIHGIHIHHIKETPGGIIKDSEKHSGPRAKSDGDGICIFGSCKVWVDHCTFDHGADGLVDVTMGGTDVTISNSIFNDHDKVMLLGVGNELEKNMKV...

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_025206`
TK1151 ID	TkA06G075420
OH-1004 ID	LXL04_025206
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_025206

Location Chr05:107549903-107551531 (-)

Description Similar to Pectate lyase 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g01270`	Probable pectate lyase 7.	No verified direct reference in this release
`At2g02720`	Probable pectate lyase 6.	No verified direct reference in this release
`At1g14420`	Probable pectate lyase that may be involved in pollen tube growth.	Two Arabidopsis late pollen transcripts are detected in cytoplasmic granules.2017 · DOI: 10.1002/pld3.12

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_025206 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009664 plant-type cell wall organization Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0030570 pectate lyase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G14420

ath:AT2G02720

ath:AT3G01270

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.

Extracellular0.675

Rank 1 · LXL04_025206 · OH-1004

Lysosome / Vacuole0.108

Rank 2 · LXL04_025206 · OH-1004

Cytoplasm0.106

Rank 3 · LXL04_025206 · OH-1004

Cell membrane0.081

Rank 4 · LXL04_025206 · OH-1004

Endoplasmic reticulum0.080

Rank 5 · LXL04_025206 · 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_4127-327 aa

PF13229.13Beta_helix151-271 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025206	`PF00544.26`	Pectate_lyase_4	127	327	3.4e-22	79.7
LXL04_025206	`PF13229.13`	Beta_helix	151	271	2.4e-08	34.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SRH4`	Arabidopsis thaliana	Probable pectate lyase 7	55.278%	Swiss-Prot	strong database homology
`O64510`	Arabidopsis thaliana	Probable pectate lyase 6	55.228%	Swiss-Prot	strong database homology
`Q9M9S2`	Arabidopsis thaliana	Probable pectate lyase 3	54.047%	Swiss-Prot	strong database homology

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