LXL04_002397 | RubberDandelionOmics

Gene overview

LXL04_002397

Reference: OH-1004 Chr: Chr01 Coordinates: 47883151-47885648 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1149 bp · LXL04_002397|LXL04_002397|OH1004|cDNA

ATGAAAATGACGGCGGCGGAGGGAGACTGCAGACAGTGGGACGAAGACGCTTACAGAGACAGCATACTGGAGGAGAGGGAATCGCATTCTCTCACCATCTTCCGAACTGCCTTCTCCCCGTCACCTACCTGCCAAAACCCTAAATTCATCGTCGCTGCCGCTAGCGATGGTTCCATCGCTACATACTCTTTATCCTCTCAAATCTCCTCCACCCCTTTAGGTTTTGGAAATTCAAAGACTCAAAATTTATCTGTAGCTGA...

CDS

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1149 bp · LXL04_002397|LXL04_002397|OH1004|CDS

ATGAAAATGACGGCGGCGGAGGGAGACTGCAGACAGTGGGACGAAGACGCTTACAGAGACAGCATACTGGAGGAGAGGGAATCGCATTCTCTCACCATCTTCCGAACTGCCTTCTCCCCGTCACCTACCTGCCAAAACCCTAAATTCATCGTCGCTGCCGCTAGCGATGGTTCCATCGCTACATACTCTTTATCCTCTCAAATCTCCTCCACCCCTTTAGGTTTTGGAAATTCAAAGACTCAAAATTTATCTGTAGCTGA...

Protein

Download Protein FASTA

382 aa · LXL04_002397|LXL04_002397|OH1004|PROTEIN

MKMTAAEGDCRQWDEDAYRDSILEERESHSLTIFRTAFSPSPTCQNPKFIVAAASDGSIATYSLSSQISSTPLGFGNSKTQNLSVAEPNCLLHGHDGPAYDVKFYGDDEDSLLLSCGDDGRIRGWKWTDVLEADKDSLSQSEGQKPKLELANPQHKGPWGALSPIPETNAIAVDTQGGSIYAAAGDSCAYCWDVEESKIKMTFKGHAGYLHSIVARNSCNQIITGSEDGTARIWDCRSGKCSNVIEPWKDKKSKDFFSYV...

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_002397`
TK1151 ID	TkAUNG043760
OH-1004 ID	LXL04_002397
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_002397

Location Chr01:47883151-47885648 (+)

Description Similar to THO6: THO complex subunit 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g19430`	Acts as a component of the THO subcomplex of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export.	DWA1 and DWA2, two Arabidopsis DWD protein components of CUL4-based E3 ligases, act together as negative regulators in ABA signal transduction.2010 · DOI: 10.1105/tpc.109.073783

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002397 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0006406 mRNA export from nucleus Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0000346 transcription export complex Cellular Component

GO:0000347 THO complex Cellular Component

GO:0000445 THO complex part of transcription export complex Cellular Component

GO:0000781 chromosome, telomeric region Cellular Component

KEGG gene cross-reference

ath:AT2G19430

dre:100004014

hsa:79228

mmu:386612

rno:79227

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.

Nucleus0.602

Rank 1 · LXL04_002397 · OH-1004

Cytoplasm0.348

Rank 2 · LXL04_002397 · OH-1004

Cell membrane0.070

Rank 3 · LXL04_002397 · OH-1004

Lysosome / Vacuole0.048

Rank 4 · LXL04_002397 · OH-1004

Endoplasmic reticulum0.041

Rank 5 · LXL04_002397 · 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.

PF24105.2Beta-prop_CAF1B_HIR1100-246 aa

PF25178.1Beta-prop_WDR41146-286 aa

PF24817.2WD40_WDHD1_1st168-276 aa

PF25173.2Beta-prop_WDR3_1st169-284 aa

PF25175.2Beta-prop_WDR5169-251 aa

PF25174.2Beta-prop_THOC3169-246 aa

PF24796.2WDR55170-289 aa

PF24805.2EIF3I171-246 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002397	`PF24105.2`	Beta-prop_CAF1B_HIR1	100	246	8.9e-08	32.2
LXL04_002397	`PF25178.1`	Beta-prop_WDR41	146	286	6.8e-11	42.3
LXL04_002397	`PF24817.2`	WD40_WDHD1_1st	168	276	1e-13	51.9
LXL04_002397	`PF25173.2`	Beta-prop_WDR3_1st	169	284	1.3e-17	64.8
LXL04_002397	`PF25175.2`	Beta-prop_WDR5	169	251	3.3e-17	63.4
LXL04_002397	`PF25174.2`	Beta-prop_THOC3	169	246	1.7e-15	57.5
LXL04_002397	`PF24796.2`	WDR55	170	289	2.9e-12	47.0
LXL04_002397	`PF24805.2`	EIF3I	171	246	1.6e-10	41.3
LXL04_002397	`PF23381.2`	Beta-prop_IFT122_1st	174	241	2.7e-16	60.4
LXL04_002397	`PF24807.2`	WD40_CDC20-Fz	176	307	1.5e-07	31.7
LXL04_002397	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	177	327	4.4e-07	30.3
LXL04_002397	`PF24814.2`	WD40_Prp19	178	308	9.4e-16	58.4
LXL04_002397	`PF25391.2`	WD40_Gbeta	179	245	1.2e-07	31.8
LXL04_002397	`PF25047.1`	Beta-prop_TEP1_2nd	181	238	1.1e-07	32.0
LXL04_002397	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	183	299	6.7e-09	36.2
LXL04_002397	`PF00400.39`	WD40	199	235	1.6e-16	60.7

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
`Q8L4M1`	Arabidopsis thaliana	THO complex subunit 6	60.109%	Swiss-Prot	strong database homology

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