LXL04_032297 | RubberDandelionOmics

Gene overview

LXL04_032297

Reference: OH-1004 Chr: Chr07 Coordinates: 20047718-20049523 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

881 bp · LXL04_032297|LXL04_032297|OH1004|cDNA

ATGTTCTTGTTAGTTGGTAAACTGATTTTTTTATGTTTGACAGAGGCAATGGTACTACAATCGGCAAAAGTATCTCTATCATCCCCTCTTAAGGAACTTGAGAAAGGAATCTTTCAACTGCAGCCCTTATGGAAAGAATCCCCAGCAGGTGGCCACGTCCTGCATGACATGCTCCATGGAAGAACTATAGATGGGCATTTGGGATGGGTGAGATCTATTGCATTTGATCCAAGTAATCAGTGGTTCTGTACCGGGTCTGT...

CDS

Download CDS FASTA

822 bp · LXL04_032297|LXL04_032297|OH1004|CDS

ATGTTCTTGTTAGTTGGTAAACTGATTTTTTTATGTTTGACAGAGGCAATGGTACTACAATCGGCAAAAGTATCTCTATCATCCCCTCTTAAGGAACTTGAGAAAGGAATCTTTCAACTGCAGCCCTTATGGAAAGAATCCCCAGCAGGTGGCCACGTCCTGCATGACATGCTCCATGGAAGAACTATAGATGGGCATTTGGGATGGGTGAGATCTATTGCATTTGATCCAAGTAATCAGTGGTTCTGTACCGGGTCTGT...

Protein

Download Protein FASTA

273 aa · LXL04_032297|LXL04_032297|OH1004|PROTEIN

MFLLVGKLIFLCLTEAMVLQSAKVSLSSPLKELEKGIFQLQPLWKESPAGGHVLHDMLHGRTIDGHLGWVRSIAFDPSNQWFCTGSVDRTIKGLLINAGLAASTRHTYMFSAGDDKLVKCWDLEQNKGLEAVLDKAVKLEDGGKTTLEIDQENMSIGQRDALLLFRTLCKVMKEDNDEVTTKTRIFSLELLQGLLEGVSHSFTNNFNITDFVKEMNFTGTFITGFNFTIPTNLSVCNWNFCSVFVAFYLCKFDIIILFIC...

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_032297`
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_032297

Location Chr07:20047718-20049523 (+)

Description Similar to BIG5: Brefeldin A-inhibited guanine nucleotide-exchange protein 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g43300`	Activates the ARF proteins by exchanging bound GDP for free GTP.	Effector-triggered immunity blocks pathogen degradation of an immunity-associated vesicle traffic regulator in Arabidopsis.2011 · DOI: 10.1073/pnas.1103338108
`At4g15900`	Pleiotropic regulator of glucose, stress and hormone responses.	Regulatory interaction of PRL1 WD protein with Arabidopsis SNF1-like protein kinases.1999 · DOI: 10.1073/pnas.96.9.5322 SKP1-SnRK protein kinase interactions mediate proteasomal binding of a plant SCF ubiquitin ligase.2001 · DOI: 10.1093/emboj/20.11.2742 Regulation of plant innate immunity by three proteins in a complex conserved across the plant and animal kingdoms.2007 · DOI: 10.1101/gad.1559607 Signaling from an altered cell wall to the nucleus mediates sugar-responsive growth and development in Arabidopsis thaliana.2007 · DOI: 10.1105/tpc.106.049965 Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases.2008 · DOI: 10.1105/tpc.107.055418 Modulation of O-mediated retrograde signaling by the PLEIOTROPIC RESPONSE LOCUS 1 (PRL1) protein, a central integrator of stress and energy signaling.2009 · DOI: 10.1111/j.1365-313x.2009.03935.x Pleiotropic regulatory locus 1 (PRL1) integrates the regulation of sugar responses with isoprenoid metabolism in Arabidopsis.2010 · DOI: 10.1093/mp/ssp100 Pleiotropic control of glucose and hormone responses by PRL1, a nuclear WD protein, in Arabidopsis.1998 · DOI: 10.1101/gad.12.19.3059
`At3g16650`	Pleiotropic regulator.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032297 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006396 RNA processing Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006897 endocytosis Biological Process

GO:0006955 immune response Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009749 response to glucose Biological Process

GO:0009755 hormone-mediated signaling pathway Biological Process

GO:0010154 fruit development Biological Process

GO:0010182 sugar mediated signaling pathway Biological Process

GO:0010215 cellulose microfibril organization Biological Process

GO:0016192 vesicle-mediated transport Biological Process

KEGG gene cross-reference

ani:ANIA_01208

ath:AT3G16650

ath:AT3G43300

ath:AT4G15900

spo:3361260

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.406

Rank 1 · LXL04_032297 · OH-1004

Nucleus0.345

Rank 2 · LXL04_032297 · OH-1004

Endoplasmic reticulum0.148

Rank 3 · LXL04_032297 · OH-1004

Mitochondrion0.120

Rank 4 · LXL04_032297 · OH-1004

Golgi apparatus0.098

Rank 5 · LXL04_032297 · 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.

PF00400.39WD4061-92 aa

PF12783.14Sec7-like_HUS158-214 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032297	`PF00400.39`	WD40	61	92	2.5e-12	47.5
LXL04_032297	`PF12783.14`	Sec7-like_HUS	158	214	1.5e-07	32.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4IXW2`	Arabidopsis thaliana	Brefeldin A-inhibited guanine nucleotide-exchange protein 5	76.136%	Swiss-Prot	weak database homology
`Q42384`	Arabidopsis thaliana	Protein pleiotropic regulatory locus 1	67.073%	Swiss-Prot	weak database homology
`Q39190`	Arabidopsis thaliana	Protein pleiotropic regulator PRL2	65.854%	Swiss-Prot	weak database homology

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