LXL04_036000 | RubberDandelionOmics

Gene overview

LXL04_036000

Reference: OH-1004 Chr: Chr08 Coordinates: 33755554-33757475 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

420 bp · LXL04_036000|LXL04_036000|OH1004|cDNA

ATGACGGATGTTGAAGGGAACTCAAAATTCTTTGGCATTGCCAAGTTTGAGAGTGCTGAAGATGCTGCAAAAGCAGTAGATGGTCTGAATGGGCAGAAGTTTGATGATAAAGACGGGTGTGTTGAAAAAGCACAGAAGAAGGGGAAAAGGGAACAGGAACATCTTGATGACACTATCTCTTATGAAGGCCTTAACGAGTTTTTTGCTCCTTTTGCTACCATCACTTTCTGCAAGGTAACGAGGGATCCTAATGGAACAAT...

CDS

Download CDS FASTA

420 bp · LXL04_036000|LXL04_036000|OH1004|CDS

ATGACGGATGTTGAAGGGAACTCAAAATTCTTTGGCATTGCCAAGTTTGAGAGTGCTGAAGATGCTGCAAAAGCAGTAGATGGTCTGAATGGGCAGAAGTTTGATGATAAAGACGGGTGTGTTGAAAAAGCACAGAAGAAGGGGAAAAGGGAACAGGAACATCTTGATGACACTATCTCTTATGAAGGCCTTAACGAGTTTTTTGCTCCTTTTGCTACCATCACTTTCTGCAAGGTAACGAGGGATCCTAATGGAACAAT...

Protein

Download Protein FASTA

139 aa · LXL04_036000|LXL04_036000|OH1004|PROTEIN

MTDVEGNSKFFGIAKFESAEDAAKAVDGLNGQKFDDKDGCVEKAQKKGKREQEHLDDTISYEGLNEFFAPFATITFCKVTRDPNGTIKGSGVIAFSISEEASRAQLLLHPDFDDLAQLSQFKTTKPLAKLVEAEMKKRK

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_036000`
TK1151 ID	TkA04G086020
OH-1004 ID	LXL04_036000
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.300
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_036000

Location Chr08:33755554-33757475 (-)

Description Similar to PAB4: Polyadenylate-binding protein 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g23350`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g49760`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At4g34110`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g34140`	Binds the poly(A) tail of mRNA.	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_036000 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0006413 translational initiation Biological Process

GO:0006417 regulation of translation Biological Process

GO:0006446 regulation of translational initiation Biological Process

GO:0048255 mRNA stabilization Biological Process

GO:0060211 regulation of nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:1900151 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005773 vacuole Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT1G49760

ath:AT2G23350

ath:AT4G34110

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.

Cytoplasm0.529

Rank 1 · LXL04_036000 · OH-1004

Nucleus0.304

Rank 2 · LXL04_036000 · OH-1004

Extracellular0.195

Rank 3 · LXL04_036000 · OH-1004

Mitochondrion0.051

Rank 4 · LXL04_036000 · OH-1004

Cell membrane0.044

Rank 5 · LXL04_036000 · 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.

PF00076.29RRM_12-37 aa

PF00076.29RRM_155-105 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036000	`PF00076.29`	RRM_1	2	37	5.5e-15	55.7
LXL04_036000	`PF00076.29`	RRM_1	55	105	5.5e-15	55.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O22173`	Arabidopsis thaliana	Polyadenylate-binding protein 4	49.606%	Swiss-Prot	moderate database homology
`Q9FXA2`	Arabidopsis thaliana	Polyadenylate-binding protein 8	47.656%	Swiss-Prot	moderate database homology
`P42731`	Arabidopsis thaliana	Polyadenylate-binding protein 2	42.073%	Swiss-Prot	moderate database homology
`F4HT49`	Arabidopsis thaliana	Polyadenylate-binding protein 1	34.868%	Swiss-Prot	moderate database homology

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