LXL04_007842 | RubberDandelionOmics

Gene overview

LXL04_007842

Reference: OH-1004 Chr: Chr02 Coordinates: 65409449-65411660 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1116 bp · LXL04_007842|LXL04_007842|OH1004|cDNA

AtggcggcggtggtggccggaaaacgaGCCAAGGCCACATCTAGCATGAAATATCACCTAACTACACCGGTTATCATCAAGGGATTAAGGTATATCGCATGTACAGGTCAAAAACTAACAGAGAAGCATTGGagaaacacaccaccacccactgccaccaaggccacggtggccggcggcggtggtggttaCCGGAAAGTACGAAAATCAAGTTCATGTAATAAACAGCCAAGAAAATCGAGAGAAACTCACAATTATAT...

CDS

Download CDS FASTA

1116 bp · LXL04_007842|LXL04_007842|OH1004|CDS

ATGGCGGCGGTGGTGGCCGGAAAACGAGCCAAGGCCACATCTAGCATGAAATATCACCTAACTACACCGGTTATCATCAAGGGATTAAGGTATATCGCATGTACAGGTCAAAAACTAACAGAGAAGCATTGGAGAAACACACCACCACCCACTGCCACCAAGGCCACGGTGGCCGGCGGCGGTGGTGGTTACCGGAAAGTACGAAAATCAAGTTCATGTAATAAACAGCCAAGAAAATCGAGAGAAACTCACAATTATAT...

Protein

Download Protein FASTA

371 aa · LXL04_007842|LXL04_007842|OH1004|PROTEIN

MAAVVAGKRAKATSSMKYHLTTPVIIKGLRYIACTGQKLTEKHWRNTPPPTATKATVAGGGGGYRKVRKSSSCNKQPRKSRETHNYIDIRSRSFNCGCFKGVPTAARLAAMSSSGSGSGGPSLGCSELRLEEACRSPPTATTTRMAEGRWSSPVVLVARETREREVSSAGDMRVAPSSMVVARLSSVEQLHRGGDGGRYRARVMVSEGAASAGKFATPLRSSLPHPPTLQAITDYPLLQTTPACIGRSAPPSSTSGSCQN...

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_007842`
TK1151 ID	TkA06G472730
OH-1004 ID	LXL04_007842
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	93.000
Protein coverage (%)	TK1151 100.000 / OH-1004 42.318 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_007842

Location Chr02:65409449-65411660 (-)

Description Similar to RAB5A: Ras-related protein Rab5A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g45130`	Involved in the trafficking of soluble cargo proteins from the prevacuolar compartment to the central vacuole.	No verified direct reference in this release
`At4g19640`	Endosomal protein that may be involved in endocytosis.	ARA7(Q69L) expression in transgenic Arabidopsis cells induces the formation of enlarged multivesicular bodies.2013 · DOI: 10.1093/jxb/ert125

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0631100`	Plays an important role in intracellular trafficking of seed storage proteins to the protein storage vacuoles (PSVs).	OsRab5a regulates endomembrane organization and storage protein trafficking in rice endosperm cells.2010 · DOI: 10.1111/j.1365-313x.2010.04370.x The small GTPase Rab5a is essential for intracellular transport of proglutelin from the Golgi apparatus to the protein storage vacuole and endosomal membrane organization in developing rice endosperm.2011 · DOI: 10.1104/pp.111.180505 OsVPS9A functions cooperatively with OsRAB5A to regulate post-Golgi dense vesicle-mediated storage protein trafficking to the protein storage vacuole in rice endosperm cells.2013 · DOI: 10.1093/mp/sst081 Zipcode RNA-Binding Proteins and Membrane Trafficking Proteins Cooperate to Transport Glutelin mRNAs in Rice Endosperm.2020 · DOI: 10.1105/tpc.20.00111

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_007842 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0007033 vacuole organization Biological Process

GO:0007034 vacuolar transport Biological Process

GO:0010256 endomembrane system organization Biological Process

GO:0015031 protein transport Biological Process

GO:0045324 late endosome to vacuole transport Biological Process

GO:0051028 mRNA transport Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005768 endosome Cellular Component

GO:0005769 early endosome Cellular Component

GO:0005774 vacuolar membrane Cellular Component

KEGG gene cross-reference

ath:AT4G19640

ath:AT5G45130

dosa:Os12g0631100

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.

Cytoplasm0.362

Rank 1 · LXL04_007842 · OH-1004

Nucleus0.347

Rank 2 · LXL04_007842 · OH-1004

Cell membrane0.243

Rank 3 · LXL04_007842 · OH-1004

Mitochondrion0.089

Rank 4 · LXL04_007842 · OH-1004

Endoplasmic reticulum0.074

Rank 5 · LXL04_007842 · 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.

PF00071.29Ras284-365 aa

PF08477.20Roc284-364 aa

PF00025.28Arf284-363 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007842	`PF00071.29`	Ras	284	365	1.6e-27	96.8
LXL04_007842	`PF08477.20`	Roc	284	364	4.7e-24	85.6
LXL04_007842	`PF00025.28`	Arf	284	363	3.5e-06	27.3

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
`P31582`	Arabidopsis thaliana	Ras-related protein RABF2a	85.227%	Swiss-Prot	weak database homology
`Q9SN68`	Arabidopsis thaliana	Ras-related protein RABF2b	84.091%	Swiss-Prot	weak database homology
`Q0ILQ6`	Oryza sativa subsp. japonica	Ras-related protein Rab5A	89.024%	Swiss-Prot	weak database homology

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