LXL04_021319 | RubberDandelionOmics

Gene overview

LXL04_021319

Reference: OH-1004 Chr: Chr04 Coordinates: 127299796-127302857 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2376 bp · LXL04_021319|LXL04_021319|OH1004|cDNA

ATGGTTAAAAATGGATCAGTGGATGTGGAGAGAGTGTTCATAGGAGGAGGATGCAACCGAATTGTTAACAATGTTTCCTGGGGTGCCTGCGGTTTAGTTTCTTTCGGCTCTCAAAATGCCGTCTCCATTTTTTGTCCGAAGGCTGCGAAGATATTAACTACACTACCAGGGCATAAGGCTTCAGTGAACTGTACTCATTGGCTTCCAAGCAGCAAGTTCGCATTTCAAGCTACCAGTTGGGAGAAGCATTATCTACTCTC...

CDS

Download CDS FASTA

2376 bp · LXL04_021319|LXL04_021319|OH1004|CDS

ATGGTTAAAAATGGATCAGTGGATGTGGAGAGAGTGTTCATAGGAGGAGGATGCAACCGAATTGTTAACAATGTTTCCTGGGGTGCCTGCGGTTTAGTTTCTTTCGGCTCTCAAAATGCCGTCTCCATTTTTTGTCCGAAGGCTGCGAAGATATTAACTACACTACCAGGGCATAAGGCTTCAGTGAACTGTACTCATTGGCTTCCAAGCAGCAAGTTCGCATTTCAAGCTACCAGTTGGGAGAAGCATTATCTACTCTC...

Protein

Download Protein FASTA

791 aa · LXL04_021319|LXL04_021319|OH1004|PROTEIN

MVKNGSVDVERVFIGGGCNRIVNNVSWGACGLVSFGSQNAVSIFCPKAAKILTTLPGHKASVNCTHWLPSSKFAFQATSWEKHYLLSGDAEGAIILWEFSPAEDKWSNVSQLLQSHKKGVTCITAFLTSQTEAIIASTSSDCVVNIWKIVLPSSGSDCTITCLDSLSTGLKPMVTLSLAELPGNPAHFILAMGGLDNKVHLYCGDSTGKFVRACELKGHTDWIRSLDFSLPIETNNLLLVSSSQDKGIRIWKLSLCDLDK...

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_021319`
TK1151 ID	TkA05G380210
OH-1004 ID	LXL04_021319
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	93.800
Protein coverage (%)	TK1151 99.373 / OH-1004 99.747 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_021319

Location Chr04:127299796-127302857 (-)

Description Similar to ELP2: Elongator complex protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g49540`	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).	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_021319 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002098 tRNA wobble uridine modification Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0006952 defense response Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0031349 positive regulation of defense response Biological Process

GO:0031538 negative regulation of anthocyanin metabolic process Biological Process

GO:0043248 proteasome assembly Biological Process

GO:0046425 regulation of receptor signaling pathway via JAK-STAT Biological Process

KEGG gene cross-reference

ath:AT1G49540

ddi:DDB_G0275651

mmu:58523

xtr:548516

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.

Nucleus0.654

Rank 1 · LXL04_021319 · OH-1004

Cytoplasm0.425

Rank 2 · LXL04_021319 · OH-1004

Mitochondrion0.038

Rank 3 · LXL04_021319 · OH-1004

Cell membrane0.034

Rank 4 · LXL04_021319 · OH-1004

Endoplasmic reticulum0.032

Rank 5 · LXL04_021319 · 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.

PF25175.2Beta-prop_WDR522-148 aa

PF24807.2WD40_CDC20-Fz23-149 aa

PF24814.2WD40_Prp1933-253 aa

PF25172.2Beta-prop_WDR3_2nd36-260 aa

PF25173.2Beta-prop_WDR3_1st37-149 aa

PF25047.1Beta-prop_TEP1_2nd80-253 aa

PF25175.2Beta-prop_WDR581-255 aa

PF25175.2Beta-prop_WDR5189-382 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021319	`PF25175.2`	Beta-prop_WDR5	22	148	5.8e-49	167.7
LXL04_021319	`PF24807.2`	WD40_CDC20-Fz	23	149	9.6e-31	107.9
LXL04_021319	`PF24814.2`	WD40_Prp19	33	253	1.4e-36	126.8
LXL04_021319	`PF25172.2`	Beta-prop_WDR3_2nd	36	260	8.2e-23	81.8
LXL04_021319	`PF25173.2`	Beta-prop_WDR3_1st	37	149	4.1e-41	141.4
LXL04_021319	`PF25047.1`	Beta-prop_TEP1_2nd	80	253	4.1e-19	69.5
LXL04_021319	`PF25175.2`	Beta-prop_WDR5	81	255	5.8e-49	167.7
LXL04_021319	`PF25175.2`	Beta-prop_WDR5	189	382	5.8e-49	167.7
LXL04_021319	`PF25174.2`	Beta-prop_THOC3	189	284	1.4e-45	156.2
LXL04_021319	`PF25173.2`	Beta-prop_WDR3_1st	189	254	4.1e-41	141.4
LXL04_021319	`PF23381.2`	Beta-prop_IFT122_1st	190	286	1.4e-48	166.4
LXL04_021319	`PF00400.39`	WD40	215	251	3.3e-49	164.0
LXL04_021319	`PF25174.2`	Beta-prop_THOC3	288	479	1.4e-45	156.2
LXL04_021319	`PF24105.2`	Beta-prop_CAF1B_HIR1	295	428	5.3e-19	69.2
LXL04_021319	`PF23381.2`	Beta-prop_IFT122_1st	360	488	1.4e-48	166.4
LXL04_021319	`PF25175.2`	Beta-prop_WDR5	362	476	5.8e-49	167.7

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
`F4I1S7`	Arabidopsis thaliana	Elongator complex protein 2	64.234%	Swiss-Prot	strong database homology

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