LXL04_038927 | RubberDandelionOmics

Gene overview

LXL04_038927

Reference: OH-1004 Chr: Chr09 Coordinates: 53524711-53529082 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2862 bp · LXL04_038927|LXL04_038927|OH1004|cDNA

ATGAGAAATCTGACGGCATTTTTCTTAACCATCTTTAACCATCTTAAGAAGCTACTAGTTCAGTGGTTTTGGTTGAAGAGATTGCAAGAAGTTATATTTCCGACCCCGTCAATGGAGTTCTTGACCCCATTAATGATGATGAACGACAACGAAGATTTTCAGACTCAGACACTCGATGACTTGAGCATCCGAAAGAGAAACCTTACAAATAACATCATACATAACCACAACTTTTCTAATGGTTTGCATTCATGGCATGC...

CDS

Download CDS FASTA

2862 bp · LXL04_038927|LXL04_038927|OH1004|CDS

ATGAGAAATCTGACGGCATTTTTCTTAACCATCTTTAACCATCTTAAGAAGCTACTAGTTCAGTGGTTTTGGTTGAAGAGATTGCAAGAAGTTATATTTCCGACCCCGTCAATGGAGTTCTTGACCCCATTAATGATGATGAACGACAACGAAGATTTTCAGACTCAGACACTCGATGACTTGAGCATCCGAAAGAGAAACCTTACAAATAACATCATACATAACCACAACTTTTCTAATGGTTTGCATTCATGGCATGC...

Protein

Download Protein FASTA

953 aa · LXL04_038927|LXL04_038927|OH1004|PROTEIN

MRNLTAFFLTIFNHLKKLLVQWFWLKRLQEVIFPTPSMEFLTPLMMMNDNEDFQTQTLDDLSIRKRNLTNNIIHNHNFSNGLHSWHANCCDVFLVSPSVGNSEPKACEHHHHAVVTNRNEHWQGLEQDITTRVSSGSTYTVVARVGVSGMHLEKDADVIATLRLEYQHSETKYLFITKTVVSKEKWENLEGTFVLSDKPKRVVFYLEGPAPGVNLLIESVSIYGDGQTEGCVYNQEGNIILNPEFEDGVNNWSGRGCKVA...

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_038927`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_038927

Location Chr09:53524711-53529082 (-)

Description Similar to XYN1: Endo-1,4-beta-xylanase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g58370`	Binds to and hydrolyzes insoluble and soluble xylan substrates (By similarity).	A xylanase, AtXyn1, is predominantly expressed in vascular bundles, and four putative xylanase genes were identified in the Arabidopsis thaliana genome.2002 · DOI: 10.1093/pcp/pcf088
`At1g10050`	Binds to and hydrolyzes insoluble and soluble xylan substrates.	No verified direct reference in this release
`At4g08160`	Binds to and hydrolyzes insoluble and soluble xylan substrates.	No verified direct reference in this release
`At2g14690`	Binds to and hydrolyzes insoluble and soluble xylan substrates.	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_038927 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0045493 xylan catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0031176 endo-1,4-beta-xylanase activity Molecular Function

KEGG gene cross-reference

ath:AT1G10050

ath:AT1G58370

ath:AT4G08160

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.

Cytoplasm0.195

Rank 1 · LXL04_038927 · OH-1004

Extracellular0.168

Rank 2 · LXL04_038927 · OH-1004

Lysosome / Vacuole0.162

Rank 3 · LXL04_038927 · OH-1004

Cell membrane0.148

Rank 4 · LXL04_038927 · OH-1004

Endoplasmic reticulum0.146

Rank 5 · LXL04_038927 · 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.

PF02018.24CBM_4_970-211 aa

PF02018.24CBM_4_9237-375 aa

PF02018.24CBM_4_9409-552 aa

PF00331.27Glyco_hydro_10609-867 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038927	`PF02018.24`	CBM_4_9	70	211	1.6e-64	217.1
LXL04_038927	`PF02018.24`	CBM_4_9	237	375	1.6e-64	217.1
LXL04_038927	`PF02018.24`	CBM_4_9	409	552	1.6e-64	217.1
LXL04_038927	`PF00331.27`	Glyco_hydro_10	609	867	8.5e-45	154.0

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
`A0A1P8AWH8`	Arabidopsis thaliana	Endo-1,4-beta-xylanase 1	66.118%	Swiss-Prot	strong database homology
`O80596`	Arabidopsis thaliana	Endo-1,4-beta-xylanase 2	58.553%	Swiss-Prot	strong database homology
`F4JG10`	Arabidopsis thaliana	Endo-1,4-beta-xylanase 3	65.612%	Swiss-Prot	strong database homology
`Q680B7`	Arabidopsis thaliana	Endo-1,4-beta-xylanase 4	31.971%	Swiss-Prot	weak database homology

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