LXL04_028371 | RubberDandelionOmics

Gene overview

LXL04_028371

Reference: OH-1004 Chr: Chr06 Coordinates: 39302823-39314060 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4587 bp · LXL04_028371|LXL04_028371|OH1004|cDNA

ATGGCAGCTCGGTCGTCTTTGGCCGGTATGGAGGTTCCGATTATCGGCAGCGATTCTACTAAATGGTTTAACGTCGCTGTACCTTCAACCTGTACTTCTATGCCGCCGCCTGAGCCCTTTGCTCCTCCTACTGACGACGCATCATCATGCTGCAACATTGGCTACCCTCCTACTTATTTCATTTGGAGAATAGACAAGAGTTGTCCAAATATTCTGGAGATAGTCGAATTCCACAGTTTTGAGGAATTTTCAAGGGTTGG...

CDS

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4587 bp · LXL04_028371|LXL04_028371|OH1004|CDS

ATGGCAGCTCGGTCGTCTTTGGCCGGTATGGAGGTTCCGATTATCGGCAGCGATTCTACTAAATGGTTTAACGTCGCTGTACCTTCAACCTGTACTTCTATGCCGCCGCCTGAGCCCTTTGCTCCTCCTACTGACGACGCATCATCATGCTGCAACATTGGCTACCCTCCTACTTATTTCATTTGGAGAATAGACAAGAGTTGTCCAAATATTCTGGAGATAGTCGAATTCCACAGTTTTGAGGAATTTTCAAGGGTTGG...

Protein

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1528 aa · LXL04_028371|LXL04_028371|OH1004|PROTEIN

MAARSSLAGMEVPIIGSDSTKWFNVAVPSTCTSMPPPEPFAPPTDDASSCCNIGYPPTYFIWRIDKSCPNILEIVEFHSFEEFSRVGLRIEFTSALCPFALICKNEVSSSPVNPYILYALTVTGVAYLIRLNNITSYASCTVFPPSDVVELAIQNYGDYGAITAMSATAGCLVIGGRTGLVGCFRLGILDPSDPGFLHELRDDSSLGRLWSKFSRRTIAPVKCLVCLEIQGKRLLLVLHSDGLLQVWDLLSFSRLLSYTI...

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_028371`
TK1151 ID	TkA07G147820
OH-1004 ID	LXL04_028371
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.400
Protein coverage (%)	TK1151 99.666 / OH-1004 97.513 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_028371

Location Chr06:39302823-39314060 (+)

Description Similar to NUP160: Nuclear pore complex protein NUP160

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g33410`	Contributes to the transfer of mature mRNA from the nucleus to the cytosol.	A putative Arabidopsis nucleoporin, AtNUP160, is critical for RNA export and required for plant tolerance to cold stress.2006 · DOI: 10.1128/mcb.01063-06 A loss-of-function mutation in the nucleoporin AtNUP160 indicates that normal auxin signalling is required for a proper ethylene response in Arabidopsis.2012 · DOI: 10.1093/jxb/err424 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 Nucleoporins Nup160 and Seh1 are required for disease resistance in Arabidopsis.2012 · DOI: 10.4161/psb.21426

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028371 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006406 mRNA export from nucleus Biological Process

GO:0006606 protein import into nucleus Biological Process

GO:0006913 nucleocytoplasmic transport Biological Process

GO:0006952 defense response Biological Process

GO:0006974 DNA damage response Biological Process

GO:0009409 response to cold Biological Process

GO:0009733 response to auxin Biological Process

GO:0015031 protein transport Biological Process

GO:0016973 poly(A)+ mRNA export from nucleus Biological Process

GO:0032502 developmental process Biological Process

GO:0046822 regulation of nucleocytoplasmic transport Biological Process

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

KEGG gene cross-reference

ath:AT1G33410

dme:Dmel_CG4738

hsa:23279

mmu:59015

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.

Nucleus0.758

Rank 1 · LXL04_028371 · OH-1004

Cytoplasm0.226

Rank 2 · LXL04_028371 · OH-1004

Cell membrane0.056

Rank 3 · LXL04_028371 · OH-1004

Golgi apparatus0.042

Rank 4 · LXL04_028371 · OH-1004

Lysosome / Vacuole0.039

Rank 5 · LXL04_028371 · 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.

PF11715.17Beta-prop_Nup120_16059-524 aa

PF17238.9NUP160_helical_2544-732 aa

PF23300.4HEAT_Nup120916-1066 aa

PF23354.2TPR_NUP160_120_M920-1167 aa

PF23347.1TPR_Nup160_C1218-1473 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028371	`PF11715.17`	Beta-prop_Nup120_160	59	524	3.6e-42	145.4
LXL04_028371	`PF17238.9`	NUP160_helical_2	544	732	9.2e-75	251.5
LXL04_028371	`PF23300.4`	HEAT_Nup120	916	1066	3.1e-12	47.4
LXL04_028371	`PF23354.2`	TPR_NUP160_120_M	920	1167	2.8e-34	119.4
LXL04_028371	`PF23347.1`	TPR_Nup160_C	1218	1473	1.1e-14	55.0

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
`Q9C811`	Arabidopsis thaliana	Nuclear pore complex protein NUP160	46.645%	Swiss-Prot	moderate database homology

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