TkA06G472730 | RubberDandelionOmics

Gene overview

TkA06G472730

Reference: TK1151 Chr: Chr06 Coordinates: 116911254-116911869 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

474 bp · TkA06G472730|TK1151|cDNA

TTCGCGACTCCCCTTAGGTCGTCACTCCCTCATCCGCCGACTCTACAAGCCATCGCCGACTACCCTCTTCTCCGAACCACTCCCGCAAGCATCGGCCGGTCAGCGCCTCCGTCATCCACCTCCGGATCCCGCCCAAACATCCACCTCAGTCGATTCGATTCTCATCCTTCGATTTCGCCCTTCAGTTGCAAAACGATTCTCGCCCAGGTTTTGGTTGGGGACATAAAAGCTGGTAAATCAAGTCTCGTGTTGCGCTTCGT...

CDS

Download CDS FASTA

474 bp · TkA06G472730|TK1151|CDS

TTCGCGACTCCCCTTAGGTCGTCACTCCCTCATCCGCCGACTCTACAAGCCATCGCCGACTACCCTCTTCTCCGAACCACTCCCGCAAGCATCGGCCGGTCAGCGCCTCCGTCATCCACCTCCGGATCCCGCCCAAACATCCACCTCAGTCGATTCGATTCTCATCCTTCGATTTCGCCCTTCAGTTGCAAAACGATTCTCGCCCAGGTTTTGGTTGGGGACATAAAAGCTGGTAAATCAAGTCTCGTGTTGCGCTTCGT...

Protein

Download Protein FASTA

157 aa · TkA06G472730|TK1151|PROTEIN

FATPLRSSLPHPPTLQAIADYPLLRTTPASIGRSAPPSSTSGSRPNIHLSRFDSHPSISPFSCKTILAQVLVGDIKAGKSSLVLRFVKGQFLEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSSAPMYYRGAAAAIFVYDITSAVLLSCP

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	`TkA06G472730`
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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G472730

Location Chr06:116911254-116911869 (+)

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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Cytoplasm0.452

Rank 1 · TkA06G472730 · TK1151

Nucleus0.299

Rank 2 · TkA06G472730 · TK1151

Plastid0.116

Rank 3 · TkA06G472730 · TK1151

Mitochondrion0.099

Rank 4 · TkA06G472730 · TK1151

Cell membrane0.097

Rank 5 · TkA06G472730 · TK1151

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.

PF00071Ras70-151 aa

PF08477Roc70-150 aa

PF00025Arf70-149 aa

PF01926MMR_HSR170-126 aa

PF04670Gtr1_RagA71-150 aa

PF00009GTP_EFTU95-150 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G472730	`PF00071`	Ras	70	151	9.6e-29	100.8
TkA06G472730	`PF08477`	Roc	70	150	6.2e-25	88.5
TkA06G472730	`PF00025`	Arf	70	149	1.4e-06	28.6
TkA06G472730	`PF01926`	MMR_HSR1	70	126	0.013	16.4
TkA06G472730	`PF04670`	Gtr1_RagA	71	150	0.0094	16.1
TkA06G472730	`PF00009`	GTP_EFTU	95	150	0.35	11.2

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	sp\|P31582\|RAF2A_ARATH Ras-related protein RABF2a	88.900%	Swiss-Prot	Medium
`Q9SN68`	Arabidopsis thaliana	sp\|Q9SN68\|RAF2B_ARATH Ras-related protein RABF2b	87.700%	Swiss-Prot	Medium
`Q0ILQ6`	Oryza sativa subsp. japonica	sp\|Q0ILQ6\|RAB5A_ORYSJ Ras-related protein Rab5A	89.000%	Swiss-Prot	Medium

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