LXL04_000573 | RubberDandelionOmics

Gene overview

LXL04_000573

Reference: OH-1004 Chr: Chr01 Coordinates: 10426737-10430429 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2811 bp · LXL04_000573|LXL04_000573|OH1004|cDNA

ATGTTATCTGAATTGAATAGGCGACCCATGATCGGCACAAATGATGGTTCGTTTGGAGACGAATTGGAGAACGAGTTAGGATTGTTGCTTCACGAACACAGGCGAGAAGCCGATGATCGTGAAAAGGAGCTAAACATGTATAGAAGTGGGTCGGCCCCACCTACCATAGAGGGTTCTTTGAGCGCAGTGGGTGGTTTATTTGGTAATCACAACGGAAACaacaataataacaataatcatTTAGCGTTCTCTGAGTTTGC...

CDS

Download CDS FASTA

2811 bp · LXL04_000573|LXL04_000573|OH1004|CDS

ATGTTATCTGAATTGAATAGGCGACCCATGATCGGCACAAATGATGGTTCGTTTGGAGACGAATTGGAGAACGAGTTAGGATTGTTGCTTCACGAACACAGGCGAGAAGCCGATGATCGTGAAAAGGAGCTAAACATGTATAGAAGTGGGTCGGCCCCACCTACCATAGAGGGTTCTTTGAGCGCAGTGGGTGGTTTATTTGGTAATCACAACGGAAACAACAATAATAACAATAATCATTTAGCGTTCTCTGAGTTTGC...

Protein

Download Protein FASTA

936 aa · LXL04_000573|LXL04_000573|OH1004|PROTEIN

MLSELNRRPMIGTNDGSFGDELENELGLLLHEHRREADDREKELNMYRSGSAPPTIEGSLSAVGGLFGNHNGNNNNNNNHLAFSEFAGGNGFMSEDELRADPAYLSYYYSNVNLNPRLPPPLLSKEDWRFSQRLQGAGGGSGGVGLGGIGDRRKANRTDVGGGGGGGVSLFSMPPGFNSKKQEAENSEAEKVKGSAEWGGDGLIGLPGLGLGSKQKSLAEIFQDDLTRSTTPSGHPSRPASRNTFENNEENNNNNLPTSY...

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_000573`
TK1151 ID	TkA01G602250
OH-1004 ID	LXL04_000573
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.500
Protein coverage (%)	TK1151 98.367 / OH-1004 25.107 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_000573

Location Chr01:10426737-10430429 (-)

Description Similar to APUM1: Pumilio homolog 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g29200`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At2g29140`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At2g29190`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At3g10360`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At3g20250`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	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_000573 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006417 regulation of translation Biological Process

GO:0010608 post-transcriptional regulation of gene expression Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0003730 mRNA 3'-UTR binding Molecular Function

KEGG gene cross-reference

ath:AT2G29140

ath:AT2G29190

ath:AT2G29200

ath:AT3G10360

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.720

Rank 1 · LXL04_000573 · OH-1004

Nucleus0.235

Rank 2 · LXL04_000573 · OH-1004

Cell membrane0.120

Rank 3 · LXL04_000573 · OH-1004

Lysosome / Vacuole0.065

Rank 4 · LXL04_000573 · OH-1004

Golgi apparatus0.052

Rank 5 · LXL04_000573 · 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.

PF07990.18NABP283-350 aa

PF07990.18NABP426-599 aa

PF00806.26PUF604-637 aa

PF00806.26PUF641-670 aa

PF00806.26PUF676-709 aa

PF22493.3PUF_NOP9714-792 aa

PF00806.26PUF718-742 aa

PF00806.26PUF748-783 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000573	`PF07990.18`	NABP	283	350	4.2e-56	191.8
LXL04_000573	`PF07990.18`	NABP	426	599	4.2e-56	191.8
LXL04_000573	`PF00806.26`	PUF	604	637	3.3e-82	270.0
LXL04_000573	`PF00806.26`	PUF	641	670	3.3e-82	270.0
LXL04_000573	`PF00806.26`	PUF	676	709	3.3e-82	270.0
LXL04_000573	`PF22493.3`	PUF_NOP9	714	792	1.3e-21	77.8
LXL04_000573	`PF00806.26`	PUF	718	742	3.3e-82	270.0
LXL04_000573	`PF00806.26`	PUF	748	783	3.3e-82	270.0
LXL04_000573	`PF00806.26`	PUF	787	819	3.3e-82	270.0
LXL04_000573	`PF00806.26`	PUF	823	856	3.3e-82	270.0
LXL04_000573	`PF00806.26`	PUF	868	897	3.3e-82	270.0

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9ZW07`	Arabidopsis thaliana	Pumilio homolog 1	56.360%	Swiss-Prot	strong database homology
`Q9ZW02`	Arabidopsis thaliana	Pumilio homolog 3	55.796%	Swiss-Prot	strong database homology
`Q9ZW06`	Arabidopsis thaliana	Pumilio homolog 2	55.176%	Swiss-Prot	strong database homology
`Q9SS47`	Arabidopsis thaliana	Pumilio homolog 4	57.988%	Swiss-Prot	moderate database homology
`Q9LJX4`	Arabidopsis thaliana	Pumilio homolog 5	38.657%	Swiss-Prot	moderate database homology

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