LXL04_021955 | RubberDandelionOmics

Gene overview

LXL04_021955

Reference: OH-1004 Chr: Chr04 Coordinates: 140941729-140947192 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3879 bp · LXL04_021955|LXL04_021955|OH1004|cDNA

ATGAAGAATCTGAAGCTCTCATGGGAGCTGTCATCCAACCTCCAGTTACAATCAGAAAATGAAGTGATACGTTGCACCGCTTTCGATATCGAACAGAATCGTTTCTTCTTTGCGTCTTCTGCTAACTTCATTTACACCATTCATCTTTCATCTTCTCAAAATGAAGAATCATGGGGTAAATCACCTTCAGTTCCACTGGTTGAAACCATCGATCTAGATCCTGATGACTCTATTACCTCCTTGGAGTATCTCATGGAGAA...

CDS

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3879 bp · LXL04_021955|LXL04_021955|OH1004|CDS

ATGAAGAATCTGAAGCTCTCATGGGAGCTGTCATCCAACCTCCAGTTACAATCAGAAAATGAAGTGATACGTTGCACCGCTTTCGATATCGAACAGAATCGTTTCTTCTTTGCGTCTTCTGCTAACTTCATTTACACCATTCATCTTTCATCTTCTCAAAATGAAGAATCATGGGGTAAATCACCTTCAGTTCCACTGGTTGAAACCATCGATCTAGATCCTGATGACTCTATTACCTCCTTGGAGTATCTCATGGAGAA...

Protein

Download Protein FASTA

1292 aa · LXL04_021955|LXL04_021955|OH1004|PROTEIN

MKNLKLSWELSSNLQLQSENEVIRCTAFDIEQNRFFFASSANFIYTIHLSSSQNEESWGKSPSVPLVETIDLDPDDSITSLEYLMEKEALIIGTSSGVLLLYNVDDNVTEVVGRVEGGVKSLSPSPDGDLLCIITGLGQMLVMTHDWDLLYEISLEDSDTCDQDIDSECSASWRGDGKFFATITTVQDSSHKKLKIWERDTGNLHSVSEPKSFMGETVEWMPSGAKIATVCDHKEEKKPPSVVFFERNGLQRSSFTVNNG...

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_021955`
TK1151 ID	TkA05G433210
OH-1004 ID	LXL04_021955
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.100
Protein coverage (%)	TK1151 93.532 / OH-1004 99.613 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_021955

Location Chr04:140941729-140947192 (+)

Description Similar to ELP1: Elongator complex protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g13680`	Component of the elongator complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine) (By similarity).	The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth.2005 · DOI: 10.1073/pnas.0502600102 Mutations in ABO1/ELO2, a subunit of holo-Elongator, increase abscisic acid sensitivity and drought tolerance in Arabidopsis thaliana.2006 · DOI: 10.1128/mcb.00433-06 Elongator mediates ABA responses, oxidative stress resistance and anthocyanin biosynthesis in Arabidopsis.2009 · DOI: 10.1111/j.1365-313x.2009.03931.x Plant Elongator regulates auxin-related genes during RNA polymerase II transcription elongation.2010 · DOI: 10.1073/pnas.0913559107

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021955 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002098 tRNA wobble uridine modification Biological Process

GO:0002926 tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation Biological Process

GO:0006400 tRNA modification Biological Process

GO:0006417 regulation of translation Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0007252 I-kappaB phosphorylation Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009787 regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009965 leaf morphogenesis Biological Process

KEGG gene cross-reference

ath:AT5G13680

hsa:8518

mmu:230233

ocu:100009360

rno:140934

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.

Cytoplasm0.617

Rank 1 · LXL04_021955 · OH-1004

Nucleus0.305

Rank 2 · LXL04_021955 · OH-1004

Golgi apparatus0.148

Rank 3 · LXL04_021955 · OH-1004

Lysosome / Vacuole0.083

Rank 4 · LXL04_021955 · OH-1004

Endoplasmic reticulum0.082

Rank 5 · LXL04_021955 · 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.

PF04762.19Beta-prop_ELP1_1st1-160 aa

PF04762.19Beta-prop_ELP1_1st160-322 aa

PF25174.2Beta-prop_THOC3265-425 aa

PF23797.2Beta-prop_ELP1_2nd356-659 aa

PF23925.2A-sol_ELP1685-897 aa

PF23878.2TPR_ELP1906-1067 aa

PF23936.2HB_ELP11101-1237 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021955	`PF04762.19`	Beta-prop_ELP1_1st	1	160	2.9e-80	270.6
LXL04_021955	`PF04762.19`	Beta-prop_ELP1_1st	160	322	2.9e-80	270.6
LXL04_021955	`PF25174.2`	Beta-prop_THOC3	265	425	1.3e-11	44.8
LXL04_021955	`PF23797.2`	Beta-prop_ELP1_2nd	356	659	4.6e-48	165.2
LXL04_021955	`PF23925.2`	A-sol_ELP1	685	897	3.6e-47	161.5
LXL04_021955	`PF23878.2`	TPR_ELP1	906	1067	1.4e-22	81.4
LXL04_021955	`PF23936.2`	HB_ELP1	1101	1237	3.5e-15	56.7

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
`Q9FNA4`	Arabidopsis thaliana	Elongator complex protein 1	52.822%	Swiss-Prot	strong database homology

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