LXL04_021915 | RubberDandelionOmics

Gene overview

LXL04_021915

Reference: OH-1004 Chr: Chr04 Coordinates: 140144498-140146511 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1509 bp · LXL04_021915|LXL04_021915|OH1004|cDNA

ATGGTTTTCGTTCTCTTTGTATATATTTATGCTTTTAAAATTGCTCTTAATACCATTTTCTATACATACATGTTTTCAGTCAAATCTACAAGATTCATTTTCATTTGGGGCTCGAAGATGAACTCCAATTATTCATTATCACGTACCCTTACAGACATTCTTTTTGTGGTCAACCCCACACACGATGATTGGTCAAAGAGGtttcaaatcattaatgatcTTCGGTCCGTTATTGAAAGTTTGGAAATTCTTAGAGGGGC...

CDS

Download CDS FASTA

1509 bp · LXL04_021915|LXL04_021915|OH1004|CDS

ATGGTTTTCGTTCTCTTTGTATATATTTATGCTTTTAAAATTGCTCTTAATACCATTTTCTATACATACATGTTTTCAGTCAAATCTACAAGATTCATTTTCATTTGGGGCTCGAAGATGAACTCCAATTATTCATTATCACGTACCCTTACAGACATTCTTTTTGTGGTCAACCCCACACACGATGATTGGTCAAAGAGGTTTCAAATCATTAATGATCTTCGGTCCGTTATTGAAAGTTTGGAAATTCTTAGAGGGGC...

Protein

Download Protein FASTA

502 aa · LXL04_021915|LXL04_021915|OH1004|PROTEIN

MVFVLFVYIYAFKIALNTIFYTYMFSVKSTRFIFIWGSKMNSNYSLSRTLTDILFVVNPTHDDWSKRFQIINDLRSVIESLEILRGATVEPFGSFVSNLFTKWGDLDISIELPNGSYISSVGKKYKQSLLLDVLKALKRRGGFHGIKYISHARVPILKCDSNKDNISCDISINNLTGQMKSKMLFWVNEIDGRFRDMVLLVKEWAKAHGINDPKTGTLNSYSLSLLIIFHFQTCEPPILPPLSEVYPRNMAGDLFGVRAA...

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_021915`
TK1151 ID	TkA05G434900
OH-1004 ID	LXL04_021915
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.800
Protein coverage (%)	TK1151 100.000 / OH-1004 92.231 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_021915

Location Chr04:140144498-140146511 (-)

Description Similar to HESO1: Protein HESO1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g39740`	Uridylates small RNAs to trigger their degradation.	Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis.2012 · DOI: 10.1016/j.cub.2012.02.052 The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation.2012 · DOI: 10.1016/j.cub.2012.02.051 Methylation protects microRNAs from an AGO1-associated activity that uridylates 5' RNA fragments generated by AGO1 cleavage.2014 · DOI: 10.1073/pnas.1405083111 Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis.2015 · DOI: 10.1371/journal.pgen.1005091 Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis.2015 · DOI: 10.1371/journal.pgen.1005119
`At2g45620`	UTP:RNA uridylyltransferase with a marked preference for uridine polymerization and a distributive activity for the first added nucleotides.	Uridylation prevents 3' trimming of oligoadenylated mRNAs.2013 · DOI: 10.1093/nar/gkt465 Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis.2015 · DOI: 10.1371/journal.pgen.1005091 Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis.2015 · DOI: 10.1371/journal.pgen.1005119 Uridylation and PABP Cooperate to Repair mRNA Deadenylated Ends in Arabidopsis.2016 · DOI: 10.1016/j.celrep.2016.02.060 A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing.2019 · DOI: 10.1038/s41477-019-0419-7 The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis.2021 · DOI: 10.1038/s41467-021-21382-2

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021915 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0000965 mitochondrial RNA 3'-end processing Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006397 mRNA processing Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0010605 negative regulation of macromolecule metabolic process Biological Process

GO:0031123 RNA 3'-end processing Biological Process

GO:0031124 mRNA 3'-end processing Biological Process

GO:0071044 histone mRNA catabolic process Biological Process

GO:0097222 mitochondrial mRNA polyadenylation Biological Process

GO:1900369 negative regulation of post-transcriptional gene silencing by regulatory ncRNA Biological Process

KEGG gene cross-reference

ath:AT2G39740

ath:AT2G45620

dme:Dmel_CG5732

hsa:55149

spo:2539762

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.

Cytoplasm0.499

Rank 1 · LXL04_021915 · OH-1004

Nucleus0.447

Rank 2 · LXL04_021915 · OH-1004

Cell membrane0.066

Rank 3 · LXL04_021915 · OH-1004

Endoplasmic reticulum0.065

Rank 4 · LXL04_021915 · OH-1004

Mitochondrion0.047

Rank 5 · LXL04_021915 · 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.

PF22600.3MTPAP-like_central46-184 aa

PF19088.7TUTase60-171 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021915	`PF22600.3`	MTPAP-like_central	46	184	6.8e-24	85.2
LXL04_021915	`PF19088.7`	TUTase	60	171	3.9e-06	27.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q5XET5`	Arabidopsis thaliana	Protein HESO1	54.955%	Swiss-Prot	moderate database homology
`O64642`	Arabidopsis thaliana	UTP:RNA uridylyltransferase 1	24.518%	Swiss-Prot	weak database homology

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