LXL04_015635 | RubberDandelionOmics

Gene overview

LXL04_015635

Reference: OH-1004 Chr: Chr03 Coordinates: 78343557-78345931 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

711 bp · LXL04_015635|LXL04_015635|OH1004|cDNA

ATGGGCTTGTATACATACGCCATAGGGTATACTAGTCTAAGGatggaggAAGAAGAACACGAGGTGTACGGAGGAGATATTCCAGATGTGGGTGAAATGGAAGGGGATGTTGATCCTCATCACGCCGATGTCGAGATGGCTACCGCAGACGAAGACGCCGTCAAGGAACTCGATGAGATGAAGAAACGATTGAAGGAGATGGAAGAAGAAGCAGCTGCTCTTCGCGAAATGCAAGCCAAAGTAGAAAAAGAAATGGGTGC...

CDS

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711 bp · LXL04_015635|LXL04_015635|OH1004|CDS

ATGGGCTTGTATACATACGCCATAGGGTATACTAGTCTAAGGATGGAGGAAGAAGAACACGAGGTGTACGGAGGAGATATTCCAGATGTGGGTGAAATGGAAGGGGATGTTGATCCTCATCACGCCGATGTCGAGATGGCTACCGCAGACGAAGACGCCGTCAAGGAACTCGATGAGATGAAGAAACGATTGAAGGAGATGGAAGAAGAAGCAGCTGCTCTTCGCGAAATGCAAGCCAAAGTAGAAAAAGAAATGGGTGC...

Protein

Download Protein FASTA

236 aa · LXL04_015635|LXL04_015635|OH1004|PROTEIN

MGLYTYAIGYTSLRMEEEEHEVYGGDIPDVGEMEGDVDPHHADVEMATADEDAVKELDEMKKRLKEMEEEAAALREMQAKVEKEMGAVQDPAGAAVSQASKEEVDTRSIFVGNVDYACTPEEVQQHFQSCGTVNRVTILTDKFGQPKGFAYVEFLEVEGVQEALALNESELHGRQLKVMAKRTNVPGMKQYRGRRFNPYMGYRGFRRPYVPPYFYPPYAYGKVPRFRRPSRYMPYY

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_015635`
TK1151 ID	TkA05G113870
OH-1004 ID	LXL04_015635
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)	98.700
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_015635

Location Chr03:78343557-78345931 (-)

Description Similar to PABN2: Polyadenylate-binding protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g65260`	Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product.	No verified direct reference in this release
`At5g10350`	Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product.	No verified direct reference in this release
`At5g51120`	Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product.	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_015635 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0031124 mRNA 3'-end processing Biological Process

GO:0033621 nuclear mRNA surveillance of meiosis-specific transcripts Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016604 nuclear body Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0033620 Mei2 nuclear dot complex Cellular Component

KEGG gene cross-reference

ath:AT5G10350

ath:AT5G51120

ath:AT5G65260

spo:2539733

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.

Nucleus0.771

Rank 1 · LXL04_015635 · OH-1004

Cytoplasm0.371

Rank 2 · LXL04_015635 · OH-1004

Cell membrane0.038

Rank 3 · LXL04_015635 · OH-1004

Mitochondrion0.037

Rank 4 · LXL04_015635 · OH-1004

Endoplasmic reticulum0.036

Rank 5 · LXL04_015635 · 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.

PF00076.29RRM_1109-177 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015635	`PF00076.29`	RRM_1	109	177	2.5e-17	63.2

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
`Q9FJN9`	Arabidopsis thaliana	Polyadenylate-binding protein 2	82.353%	Swiss-Prot	strong database homology
`Q9LX90`	Arabidopsis thaliana	Polyadenylate-binding protein 3	79.186%	Swiss-Prot	strong database homology
`Q93VI4`	Arabidopsis thaliana	Polyadenylate-binding protein 1	76.087%	Swiss-Prot	strong database homology

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