LXL04_029539 | RubberDandelionOmics

Gene overview

LXL04_029539

Reference: OH-1004 Chr: Chr06 Coordinates: 93433504-93435180 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1068 bp · LXL04_029539|LXL04_029539|OH1004|cDNA

ATGGAGAAATCAGTGGCAACTTTAGATAATGGGGCAATATGCTCTTCATGGAACTACTGTGGCCAAAGATTGGCTACTGGTATGATCGATGGAACAATTGCTATCTACGACACTAGTGATCCAGCTTCTTCCACATTCACCTCGACTTTTAAATTCAAGGTTAGCGAGGGAAGCATTGTAAAGGCTGTATGGGTTCCCCCGGAGTATGGCGATGCAGTTGCGTGCATATGTTCCAATGGAAGTTTATCAATCTGGGAAGA...

CDS

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1068 bp · LXL04_029539|LXL04_029539|OH1004|CDS

ATGGAGAAATCAGTGGCAACTTTAGATAATGGGGCAATATGCTCTTCATGGAACTACTGTGGCCAAAGATTGGCTACTGGTATGATCGATGGAACAATTGCTATCTACGACACTAGTGATCCAGCTTCTTCCACATTCACCTCGACTTTTAAATTCAAGGTTAGCGAGGGAAGCATTGTAAAGGCTGTATGGGTTCCCCCGGAGTATGGCGATGCAGTTGCGTGCATATGTTCCAATGGAAGTTTATCAATCTGGGAAGA...

Protein

Download Protein FASTA

355 aa · LXL04_029539|LXL04_029539|OH1004|PROTEIN

MEKSVATLDNGAICSSWNYCGQRLATGMIDGTIAIYDTSDPASSTFTSTFKFKVSEGSIVKAVWVPPEYGDAVACICSNGSLSIWEEIAEGTQCVFLGVQLYLLLYIHKPIMNLSPLSPLDSEPVQWKQRKTFAGSSNQVLDAQFGNSHPSLKLTVAYSNGLVKVYEILDQMDLKNWQLQAEFQNVTDSITKFGNTSCLSASISWNPQRSDTCSASFLLGLNSDTPQLNSPKVWEFDQDHQRWLPVAELADTDDKGDQVY...

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_029539`
TK1151 ID	TkA02G261550
OH-1004 ID	LXL04_029539
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	90.700
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_029539

Location Chr06:93433504-93435180 (-)

Description Similar to SEH1: Protein SEH1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g64350`	Required for proper export of mRNAs from the nucleus to the cytoplasm.	Putative members of the Arabidopsis Nup107-160 nuclear pore sub-complex contribute to pathogen defense.2012 · DOI: 10.1111/j.1365-313x.2012.04928.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029539 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006999 nuclear pore organization Biological Process

GO:0007080 mitotic metaphase chromosome alignment Biological Process

GO:0015031 protein transport Biological Process

GO:0031669 cellular response to nutrient levels Biological Process

GO:0034198 cellular response to amino acid starvation Biological Process

GO:0051028 mRNA transport Biological Process

GO:0051301 cell division Biological Process

GO:0051315 attachment of mitotic spindle microtubules to kinetochore Biological Process

GO:1904263 positive regulation of TORC1 signaling Biological Process

GO:0000776 kinetochore Cellular Component

GO:0005635 nuclear envelope Cellular Component

GO:0005765 lysosomal membrane Cellular Component

KEGG gene cross-reference

ath:AT1G64350

xla:444365

xla:734650

xtr:496570

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.

Cytoplasm0.572

Rank 1 · LXL04_029539 · OH-1004

Nucleus0.490

Rank 2 · LXL04_029539 · OH-1004

Lysosome / Vacuole0.064

Rank 3 · LXL04_029539 · OH-1004

Cell membrane0.058

Rank 4 · LXL04_029539 · OH-1004

Golgi apparatus0.056

Rank 5 · LXL04_029539 · 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.

PF23381.2Beta-prop_IFT122_1st9-86 aa

PF25174.2Beta-prop_THOC316-86 aa

PF25173.2Beta-prop_WDR3_1st228-338 aa

PF23381.2Beta-prop_IFT122_1st254-340 aa

PF25174.2Beta-prop_THOC3257-339 aa

PF24807.2WD40_CDC20-Fz257-340 aa

PF25175.2Beta-prop_WDR5258-340 aa

PF12894.14ANAPC4_WD40297-346 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029539	`PF23381.2`	Beta-prop_IFT122_1st	9	86	6.8e-13	49.3
LXL04_029539	`PF25174.2`	Beta-prop_THOC3	16	86	2.1e-14	53.9
LXL04_029539	`PF25173.2`	Beta-prop_WDR3_1st	228	338	1.1e-10	42.3
LXL04_029539	`PF23381.2`	Beta-prop_IFT122_1st	254	340	6.8e-13	49.3
LXL04_029539	`PF25174.2`	Beta-prop_THOC3	257	339	2.1e-14	53.9
LXL04_029539	`PF24807.2`	WD40_CDC20-Fz	257	340	1.6e-08	34.9
LXL04_029539	`PF25175.2`	Beta-prop_WDR5	258	340	1.3e-06	28.6
LXL04_029539	`PF12894.14`	ANAPC4_WD40	297	346	4.2e-10	40.5
LXL04_029539	`PF00400.39`	WD40	302	337	7.5e-14	52.3

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
`Q93VR9`	Arabidopsis thaliana	Protein SEH1	54.830%	Swiss-Prot	strong database homology

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