LXL04_018693 | RubberDandelionOmics

Gene overview

LXL04_018693

Reference: OH-1004 Chr: Chr04 Coordinates: 16756876-16760889 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1326 bp · LXL04_018693|LXL04_018693|OH1004|cDNA

ATGGCGGTTTCTCTGAGATTAATCGCGCTCTGCTCATTGCTACTACTTGCGCTTGTTGTGTCCATCAATGCGGTTTATAGTGAAGATAAAGAGAAACAGGAGTTGCAGAGCTTAGTAAGCAACGCCACAATTGCAGACAGGACAACCGAAAACCTTGCTATAAGAACGAATGGCGATGCTGTTGATGACGATCCAGATATGGTAGCTTCCATGGTTGACAAGAGCATTCGTAACAGTACAGAGAGGAGGAAATTGGGGTA...

CDS

Download CDS FASTA

1326 bp · LXL04_018693|LXL04_018693|OH1004|CDS

ATGGCGGTTTCTCTGAGATTAATCGCGCTCTGCTCATTGCTACTACTTGCGCTTGTTGTGTCCATCAATGCGGTTTATAGTGAAGATAAAGAGAAACAGGAGTTGCAGAGCTTAGTAAGCAACGCCACAATTGCAGACAGGACAACCGAAAACCTTGCTATAAGAACGAATGGCGATGCTGTTGATGACGATCCAGATATGGTAGCTTCCATGGTTGACAAGAGCATTCGTAACAGTACAGAGAGGAGGAAATTGGGGTA...

Protein

Download Protein FASTA

441 aa · LXL04_018693|LXL04_018693|OH1004|PROTEIN

MAVSLRLIALCSLLLLALVVSINAVYSEDKEKQELQSLVSNATIADRTTENLAIRTNGDAVDDDPDMVASMVDKSIRNSTERRKLGYFSCGTGNPMDDCWRCDPNWQRHRKRLADCAIGFGRNAVGGRDGRFYVVTNPNDDNAVNPKPGTLRHAVIQDKPLWIVFKRDMVITLKQELIMNSFKTIDARGVNVHIANGACITIQYVTNIIIHGLHIHDCKPTGNAMVRSSPSHYGWRTMADGDGISLFGASHVWIDHNSLS...

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_018693`
TK1151 ID	TkA08G078080
OH-1004 ID	LXL04_018693
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.800
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_018693

Location Chr04:16756876-16760889 (+)

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
`At3g07010`	Probable pectate lyase 8.	No verified direct reference in this release
`At1g04680`	Probable pectate lyase 1.	No verified direct reference in this release
`At3g24670`	Probable pectate lyase 10.	No verified direct reference in this release
`At5g48900`	Probable pectate lyase 20.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_018693 · 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:AT3G24670

ath:AT4G13710

ath:AT5G48900

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.

Extracellular0.687

Rank 1 · LXL04_018693 · OH-1004

Lysosome / Vacuole0.092

Rank 2 · LXL04_018693 · OH-1004

Cytoplasm0.081

Rank 3 · LXL04_018693 · OH-1004

Endoplasmic reticulum0.058

Rank 4 · LXL04_018693 · OH-1004

Cell membrane0.054

Rank 5 · LXL04_018693 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00544.26Pectate_lyase_4179-373 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018693	`PF00544.26`	Pectate_lyase_4	179	373	3.7e-18	66.4

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
`Q944R1`	Arabidopsis thaliana	Probable pectate lyase 15	75.721%	Swiss-Prot	strong database homology
`Q9M8Z8`	Arabidopsis thaliana	Probable pectate lyase 8	73.982%	Swiss-Prot	strong database homology
`Q940Q1`	Arabidopsis thaliana	Probable pectate lyase 1	73.953%	Swiss-Prot	strong database homology
`Q9LJ42`	Arabidopsis thaliana	Probable pectate lyase 10	72.624%	Swiss-Prot	strong database homology
`Q93WF1`	Arabidopsis thaliana	Probable pectate lyase 20	72.398%	Swiss-Prot	strong database homology

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