LXL04_030381 | RubberDandelionOmics

Gene overview

LXL04_030381

Reference: OH-1004 Chr: Chr06 Coordinates: 115100496-115102535 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1671 bp · LXL04_030381|LXL04_030381|OH1004|cDNA

ATGAAGCCTCAGAGAAACTCCCACATAATACAAACTCCACCGCATCATTACGCAATCGGAGAGGAAGCTACGTTTCAGTCTTTTTCGCCGTGGGTTATCGCCGATGCCGGCGTTTTGCCGGGGTATGATCGGCATCAGATGCCGTCTAACCTTCCTCCGTCAGTCGATGTGGGTGAAGATGTATGTAGTGCATTCTCTTCACTCAATATCTCCCCCACCACTCACATCCACAGTCCGAAGATCGTTCCGGAGAATCTCTA...

CDS

Download CDS FASTA

1671 bp · LXL04_030381|LXL04_030381|OH1004|CDS

ATGAAGCCTCAGAGAAACTCCCACATAATACAAACTCCACCGCATCATTACGCAATCGGAGAGGAAGCTACGTTTCAGTCTTTTTCGCCGTGGGTTATCGCCGATGCCGGCGTTTTGCCGGGGTATGATCGGCATCAGATGCCGTCTAACCTTCCTCCGTCAGTCGATGTGGGTGAAGATGTATGTAGTGCATTCTCTTCACTCAATATCTCCCCCACCACTCACATCCACAGTCCGAAGATCGTTCCGGAGAATCTCTA...

Protein

Download Protein FASTA

556 aa · LXL04_030381|LXL04_030381|OH1004|PROTEIN

MKPQRNSHIIQTPPHHYAIGEEATFQSFSPWVIADAGVLPGYDRHQMPSNLPPSVDVGEDVCSAFSSLNISPTTHIHSPKIVPENLYAKSRGFGSPIGIGEGSVHPFRSEIGLVAVNSGNSNRRIYSSVGHPHQFTVDPSQHNQPPLWRNRDVLHQVRSSGFDFDQPSDLLPTEQLNPHFLCSSNPSAQIIDDTFVQNTMNNSSFSTPITDNLNLATTKFRNYQLLSFLSLKELRGRIRSLAKDQNGCRLLQSKFENPTA...

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_030381`
TK1151 ID	TkA07G400580
OH-1004 ID	LXL04_030381
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 91.727 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_030381

Location Chr06:115100496-115102535 (+)

Description Similar to APUM12: Pumilio homolog 12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g56510`	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
`At1g22240`	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
`At1g78160`	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
`At1g35730`	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
`At4g08840`	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_030381 · 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:1902039 negative regulation of seed dormancy process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G22240

ath:AT1G35730

ath:AT1G78160

ath:AT4G08840

ath:AT5G56510

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.

Cytoplasm0.631

Rank 1 · LXL04_030381 · OH-1004

Nucleus0.379

Rank 2 · LXL04_030381 · OH-1004

Cell membrane0.116

Rank 3 · LXL04_030381 · OH-1004

Endoplasmic reticulum0.042

Rank 4 · LXL04_030381 · OH-1004

Lysosome / Vacuole0.034

Rank 5 · LXL04_030381 · 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.

PF00806.26PUF238-267 aa

PF00806.26PUF274-303 aa

PF22493.3PUF_NOP9319-432 aa

PF00806.26PUF352-382 aa

PF00806.26PUF385-419 aa

PF00806.26PUF461-491 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030381	`PF00806.26`	PUF	238	267	4.8e-61	202.4
LXL04_030381	`PF00806.26`	PUF	274	303	4.8e-61	202.4
LXL04_030381	`PF22493.3`	PUF_NOP9	319	432	3.7e-16	59.8
LXL04_030381	`PF00806.26`	PUF	352	382	4.8e-61	202.4
LXL04_030381	`PF00806.26`	PUF	385	419	4.8e-61	202.4
LXL04_030381	`PF00806.26`	PUF	461	491	4.8e-61	202.4

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9LVC3`	Arabidopsis thaliana	Pumilio homolog 12	39.944%	Swiss-Prot	moderate database homology
`Q9LM20`	Arabidopsis thaliana	Putative pumilio homolog 8, chloroplastic	42.405%	Swiss-Prot	moderate database homology
`Q9C9R6`	Arabidopsis thaliana	Putative pumilio homolog 7, chloroplastic	40.625%	Swiss-Prot	moderate database homology
`Q1PFN9`	Arabidopsis thaliana	Pumilio homolog 9	40.125%	Swiss-Prot	moderate database homology
`Q9LDW3`	Arabidopsis thaliana	Pumilio homolog 11	39.564%	Swiss-Prot	moderate database homology

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