LXL04_022727 | RubberDandelionOmics

Gene overview

LXL04_022727

Reference: OH-1004 Chr: Chr05 Coordinates: 6968671-6975358 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5298 bp · LXL04_022727|LXL04_022727|OH1004|cDNA

ATGGCTTCTGCGGAAGCCGAATCCCGTCTCATCAACAGCATTTTAGTCCCCGCGCTAGAAAAAATCATCAAAAATGGTTCATGGCGGAAACACTCTAAGCTTGTACGTCAGTGTAAATCCGTACTAGGACGCATTTCCTCCCCGGATAACCCCCCTCCCCCTTCCCCTCTCTCCACCCCTTGCACCCCTCCCACCCCGGAGGAATTTCAATCAGGCGTCGACTTGCCGTCTCAAGGCGTTCTACATGATTCCGGAACGAA...

CDS

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5298 bp · LXL04_022727|LXL04_022727|OH1004|CDS

ATGGCTTCTGCGGAAGCCGAATCCCGTCTCATCAACAGCATTTTAGTCCCCGCGCTAGAAAAAATCATCAAAAATGGTTCATGGCGGAAACACTCTAAGCTTGTACGTCAGTGTAAATCCGTACTAGGACGCATTTCCTCCCCGGATAACCCCCCTCCCCCTTCCCCTCTCTCCACCCCTTGCACCCCTCCCACCCCGGAGGAATTTCAATCAGGCGTCGACTTGCCGTCTCAAGGCGTTCTACATGATTCCGGAACGAA...

Protein

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1765 aa · LXL04_022727|LXL04_022727|OH1004|PROTEIN

MASAEAESRLINSILVPALEKIIKNGSWRKHSKLVRQCKSVLGRISSPDNPPPPSPLSTPCTPPTPEEFQSGVDLPSQGVLHDSGTNELTLYESKFVLSPIITACSSETLKIVEPALDCIQKLIAHGCIRGESDPTGGPDAKLLAKLIESVCKCHELGDEGVELLVLKTILSAVTSVALRIHGDSLLRIVRTSYDIYLQSKNVVNQTTAKASLIQMLVIVFRRMEADSSTELVHPIVVAELMEPVEKTDDGDGTMTMFVQ...

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_022727`
TK1151 ID	TkA06G457360
OH-1004 ID	LXL04_022727
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / OH-1004 58.810 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_022727

Location Chr05:6968671-6975358 (-)

Description Similar to BIG2: Brefeldin A-inhibited guanine nucleotide-exchange protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g60860`	Activates the ARF proteins by exchanging bound GDP for free GTP.	No verified direct reference in this release
`At1g01960`	Activates the ARF proteins by exchanging bound GDP for free GTP.	No verified direct reference in this release
`At4g38200`	Activates the ARF proteins by exchanging bound GDP for free GTP.	No verified direct reference in this release
`At4g35380`	Activates the ARF proteins by exchanging bound GDP for free GTP.	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_022727 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001881 receptor recycling Biological Process

GO:0006887 exocytosis Biological Process

GO:0006893 Golgi to plasma membrane transport Biological Process

GO:0007032 endosome organization Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0010256 endomembrane system organization Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0032012 regulation of ARF protein signal transduction Biological Process

GO:0032760 positive regulation of tumor necrosis factor production Biological Process

GO:0035556 intracellular signal transduction Biological Process

GO:0043001 Golgi to plasma membrane protein transport Biological Process

KEGG gene cross-reference

ath:AT1G01960

ath:AT3G60860

ath:AT4G35380

ath:AT4G38200

hsa:10564

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.

Cytoplasm0.474

Rank 1 · LXL04_022727 · OH-1004

Golgi apparatus0.385

Rank 2 · LXL04_022727 · OH-1004

Cell membrane0.172

Rank 3 · LXL04_022727 · OH-1004

Lysosome / Vacuole0.147

Rank 4 · LXL04_022727 · OH-1004

Nucleus0.142

Rank 5 · LXL04_022727 · 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.

PF16213.12DCB13-227 aa

PF12783.14Sec7-like_HUS359-517 aa

PF01369.26Sec7626-807 aa

PF09324.16Sec7-like_HDS1170-1252 aa

PF16206.10Mon2_C1269-1419 aa

PF23325.2TPR_281353-1458 aa

PF20252.4BIG2_C1562-1753 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022727	`PF16213.12`	DCB	13	227	4.5e-37	128.2
LXL04_022727	`PF12783.14`	Sec7-like_HUS	359	517	1.9e-48	165.1
LXL04_022727	`PF01369.26`	Sec7	626	807	1e-76	257.4
LXL04_022727	`PF09324.16`	Sec7-like_HDS	1170	1252	1.9e-29	102.0
LXL04_022727	`PF16206.10`	Mon2_C	1269	1419	4.7e-08	32.4
LXL04_022727	`PF23325.2`	TPR_28	1353	1458	1.2e-07	32.5
LXL04_022727	`PF20252.4`	BIG2_C	1562	1753	7.9e-40	137.5

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
`Q9LZX8`	Arabidopsis thaliana	Brefeldin A-inhibited guanine nucleotide-exchange protein 2	68.691%	Swiss-Prot	strong database homology
`Q9LPC5`	Arabidopsis thaliana	Brefeldin A-inhibited guanine nucleotide-exchange protein 3	67.151%	Swiss-Prot	strong database homology
`F4JSZ5`	Arabidopsis thaliana	Brefeldin A-inhibited guanine nucleotide-exchange protein 1	46.038%	Swiss-Prot	moderate database homology
`F4JN05`	Arabidopsis thaliana	Brefeldin A-inhibited guanine nucleotide-exchange protein 4	46.059%	Swiss-Prot	moderate database homology

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