LXL04_009407 | RubberDandelionOmics

Gene overview

LXL04_009407

Reference: OH-1004 Chr: Chr02 Coordinates: 125462342-125464314 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1344 bp · LXL04_009407|LXL04_009407|OH1004|cDNA

ATGAAGGAAGCATTGGTGGTTTGCGGAGAGAAGAACTTAACGGTGGGACTGACGATTTGGGACATAGAAACAGGGGATCATCTTCTTCACATACCCACATGTGCTTCACACTTCCATGGGCTCACTTGTTTGAGAAATCAGTACTTGGTTGCCTCTCAAATTCACCGCCCTGGCTCCGTCGCCGGCGGCGTCGTCTTCACCTGGCCTTTCTCCAAGCCTCGTTCACCATTACGGAGCTATACAGTTGAAGCCATTGGGCC...

CDS

Download CDS FASTA

1344 bp · LXL04_009407|LXL04_009407|OH1004|CDS

ATGAAGGAAGCATTGGTGGTTTGCGGAGAGAAGAACTTAACGGTGGGACTGACGATTTGGGACATAGAAACAGGGGATCATCTTCTTCACATACCCACATGTGCTTCACACTTCCATGGGCTCACTTGTTTGAGAAATCAGTACTTGGTTGCCTCTCAAATTCACCGCCCTGGCTCCGTCGCCGGCGGCGTCGTCTTCACCTGGCCTTTCTCCAAGCCTCGTTCACCATTACGGAGCTATACAGTTGAAGCCATTGGGCC...

Protein

Download Protein FASTA

447 aa · LXL04_009407|LXL04_009407|OH1004|PROTEIN

MKEALVVCGEKNLTVGLTIWDIETGDHLLHIPTCASHFHGLTCLRNQYLVASQIHRPGSVAGGVVFTWPFSKPRSPLRSYTVEAIGPLSSTNDGIYLAGGAISGNAYIWEVINGKLLKTWHAHNSPITCLAFSNDSSLLISASEDGMIVVWPMISLLDDKYSEPSHLSLNVTTDHKSFITGLLPSCNVSQSVFVSSSLDGTCKAWDIIKGTLLQTWSFPQPITATVLDPLERFLFCGSADGRIFMTSFDVGLMTEPCVDL...

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_009407`
TK1151 ID	TkA03G434460
OH-1004 ID	LXL04_009407
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_009407

Location Chr02:125462342-125464314 (+)

Description Similar to RID3: Protein ROOT INITIATION DEFECTIVE 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g49180`	Involved in meristem development.	Identification of novel meristem factors involved in shoot regeneration through the analysis of temperature-sensitive mutants of Arabidopsis.2009 · DOI: 10.1111/j.1365-313x.2008.03750.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009407 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006261 DNA-templated DNA replication Biological Process

GO:0006364 rRNA processing Biological Process

GO:0007368 determination of left/right symmetry Biological Process

GO:1902184 negative regulation of shoot apical meristem development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005656 nuclear pre-replicative complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0080008 Cul4-RING E3 ubiquitin ligase complex Cellular Component

GO:0120293 dynein axonemal particle Cellular Component

KEGG gene cross-reference

ath:AT3G49180

bta:533356

dre:445819

hsa:57418

xla:733228

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.

Cytoplasm0.539

Rank 1 · LXL04_009407 · OH-1004

Nucleus0.309

Rank 2 · LXL04_009407 · OH-1004

Lysosome / Vacuole0.099

Rank 3 · LXL04_009407 · OH-1004

Cell membrane0.086

Rank 4 · LXL04_009407 · OH-1004

Golgi apparatus0.086

Rank 5 · LXL04_009407 · 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.

PF23414.2Beta-prop_EML_264-181 aa

PF25173.2Beta-prop_WDR3_1st82-151 aa

PF24807.2WD40_CDC20-Fz85-211 aa

PF25173.2Beta-prop_WDR3_1st86-243 aa

PF24817.2WD40_WDHD1_1st88-153 aa

PF25174.2Beta-prop_THOC390-152 aa

PF23381.2Beta-prop_IFT122_1st92-245 aa

PF29037.1DSE1_N92-159 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009407	`PF23414.2`	Beta-prop_EML_2	64	181	2.2e-17	64.1
LXL04_009407	`PF25173.2`	Beta-prop_WDR3_1st	82	151	1.3e-39	136.5
LXL04_009407	`PF24807.2`	WD40_CDC20-Fz	85	211	1.7e-16	61.1
LXL04_009407	`PF25173.2`	Beta-prop_WDR3_1st	86	243	1.3e-39	136.5
LXL04_009407	`PF24817.2`	WD40_WDHD1_1st	88	153	1.5e-17	64.4
LXL04_009407	`PF25174.2`	Beta-prop_THOC3	90	152	7.6e-21	75.0
LXL04_009407	`PF23381.2`	Beta-prop_IFT122_1st	92	245	8.6e-21	75.2
LXL04_009407	`PF29037.1`	DSE1_N	92	159	2.8e-09	37.3
LXL04_009407	`PF24782.3`	WD40_MABP1-WDR62_2nd	93	151	5.5e-06	26.3
LXL04_009407	`PF25175.2`	Beta-prop_WDR5	94	152	1.1e-26	94.6
LXL04_009407	`PF24814.2`	WD40_Prp19	94	217	2.6e-20	73.3
LXL04_009407	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	96	151	6.7e-11	42.8
LXL04_009407	`PF24796.2`	WDR55	97	246	1.1e-10	41.8
LXL04_009407	`PF23393.3`	Beta-prop_WDR90_POC16_2nd	97	152	3.3e-09	37.1
LXL04_009407	`PF23409.2`	Beta-prop_EML	97	152	2e-07	31.5
LXL04_009407	`PF23383.2`	Beta-prop_IFT140_1st	97	152	4.3e-06	26.4

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
`Q9M3B4`	Arabidopsis thaliana	Protein ROOT INITIATION DEFECTIVE 3	30.952%	Swiss-Prot	moderate database homology

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