LXL04_027250 | RubberDandelionOmics

Gene overview

LXL04_027250

Reference: OH-1004 Chr: Chr06 Coordinates: 11822135-11823045 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

607 bp · LXL04_027250|LXL04_027250|OH1004|cDNA

ATTGCTATCAGATTGCGGTTACTGAGTTACCAGTTAGATCAGCAAAGTTCATAGCACGCAAACAGTGGGTTGTTGCGGGTGCAGATGACATGTACATCCGTGTATACAACTACAACACAATGGATAAAGTCAAAGTATACGAGGCGCATACAGATTATATTAGATGTGTGGTTGTGCACCCTAAAGACACCAACACTTTTGCAAGTGCATCACTTGATCGTACCATAAAGTGCATCCCAATAATTATCACAGGTTCTGAA...

CDS

Download CDS FASTA

453 bp · LXL04_027250|LXL04_027250|OH1004|CDS

ATGTACATCCGTGTATACAACTACAACACAATGGATAAAGTCAAAGTATACGAGGCGCATACAGATTATATTAGATGTGTGGTTGTGCACCCTAAAGACACCAACACTTTTGCAAGTGCATCACTTGATCGTACCATAAAGTGCATCCCAATAATTATCACAGGTTCTGAAGATGGTACTGTACGTATATGGCACTCAACTACTTATAGGCTAGAGAACACATTGAACTATGGACTTGAAAGGGTGTGGGCTGTTGGCTG...

Protein

Download Protein FASTA

150 aa · LXL04_027250|LXL04_027250|OH1004|PROTEIN

MYIRVYNYNTMDKVKVYEAHTDYIRCVVVHPKDTNTFASASLDRTIKCIPIIITGSEDGTVRIWHSTTYRLENTLNYGLERVWAVGCMKGSRRVVFRYDKGTIMVKIGREEPVVSMDNSGKIIWSKHNEIQTVNIKIIFCLMTYYGLMDL

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_027250`
TK1151 ID	TkA06G077740
OH-1004 ID	LXL04_027250
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	95.800
Protein coverage (%)	TK1151 81.197 / OH-1004 63.333 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_027250

Location Chr06:11822135-11823045 (+)

Description Similar to Os02g0209100: Coatomer subunit beta'-2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g52360`	The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network.	No verified direct reference in this release
`At1g79990`	The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0209100`	The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network.	No verified direct reference in this release
`Os02g0209000`	The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network.	No verified direct reference in this release
`Os06g0143900`	The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027250 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport Biological Process

GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Biological Process

GO:0006891 intra-Golgi vesicle-mediated transport Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0030126 COPI vesicle coat Cellular Component

GO:0005198 structural molecule activity Molecular Function

KEGG gene cross-reference

ath:AT1G52360

ath:AT1G79990

dosa:Os02g0209000

dosa:Os02g0209100

dosa:Os06g0143900

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.

Nucleus0.514

Rank 1 · LXL04_027250 · OH-1004

Cytoplasm0.417

Rank 2 · LXL04_027250 · OH-1004

Cell membrane0.058

Rank 3 · LXL04_027250 · OH-1004

Lysosome / Vacuole0.056

Rank 4 · LXL04_027250 · OH-1004

Endoplasmic reticulum0.047

Rank 5 · LXL04_027250 · 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_1st3-47 aa

PF25174.2Beta-prop_THOC33-48 aa

PF25175.2Beta-prop_WDR53-47 aa

PF24814.2WD40_Prp193-76 aa

PF00400.39WD4013-48 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027250	`PF23381.2`	Beta-prop_IFT122_1st	3	47	4.1e-10	40.2
LXL04_027250	`PF25174.2`	Beta-prop_THOC3	3	48	2.9e-09	37.1
LXL04_027250	`PF25175.2`	Beta-prop_WDR5	3	47	2.9e-09	37.3
LXL04_027250	`PF24814.2`	WD40_Prp19	3	76	2.1e-06	27.7
LXL04_027250	`PF00400.39`	WD40	13	48	1.5e-11	45.0

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
`Q9C827`	Arabidopsis thaliana	Coatomer subunit beta'-2	46.429%	Swiss-Prot	moderate database homology
`Q9CAA0`	Arabidopsis thaliana	Coatomer subunit beta'-1	45.635%	Swiss-Prot	moderate database homology
`Q6H8D5`	Oryza sativa subsp. japonica	Coatomer subunit beta'-2	47.619%	Swiss-Prot	moderate database homology
`Q6H8D6`	Oryza sativa subsp. japonica	Putative coatomer subunit beta'-3	47.619%	Swiss-Prot	moderate database homology
`Q5VQ78`	Oryza sativa subsp. japonica	Coatomer subunit beta'-1	46.825%	Swiss-Prot	moderate database homology

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