TkA01G255280 | RubberDandelionOmics

Gene overview

TkA01G255280

Reference: TK1151 Chr: Chr01 Coordinates: 64382995-64383750 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

426 bp · TkA01G255280|TK1151|cDNA

ATGAGAGCCTTCGATGAGTTAAGAAAGCTGGAAATGTTTTTCAAGGAGGAAGACAGACATGGCTGTTCAGTAGTAGACCTGTATGAACTTGTCCAACATGCTGGAAACATTTTACCTAGACTGTATCTTCTATGTACAGTAGGGTCTGTTTACATAAAATCAAAAGAAGCTCCTGCTAATAGAGATGAGGATACTGTCATGGATGCTGTTGAATTTGTGCTGCAAAACTTTTCAGAAATGAACAAGCTTTGGGTCTGGAT...

CDS

Download CDS FASTA

426 bp · TkA01G255280|TK1151|CDS

ATGAGAGCCTTCGATGAGTTAAGAAAGCTGGAAATGTTTTTCAAGGAGGAAGACAGACATGGCTGTTCAGTAGTAGACCTGTATGAACTTGTCCAACATGCTGGAAACATTTTACCTAGACTGTATCTTCTATGTACAGTAGGGTCTGTTTACATAAAATCAAAAGAAGCTCCTGCTAATAGAGATGAGGATACTGTCATGGATGCTGTTGAATTTGTGCTGCAAAACTTTTCAGAAATGAACAAGCTTTGGGTCTGGAT...

Protein

Download Protein FASTA

141 aa · TkA01G255280|TK1151|PROTEIN

MRAFDELRKLEMFFKEEDRHGCSVVDLYELVQHAGNILPRLYLLCTVGSVYIKSKEAPANRDEDTVMDAVEFVLQNFSEMNKLWVWMEVQGPARVRDKMEKERNELRDLFIFDCRLLLQKIYIAKRKLERAISSLPKKHID

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	`TkA01G255280`
TK1151 ID	TkA01G255280
OH-1004 ID	LXL04_015068
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	98.600
Protein coverage (%)	TK1151 100.000 / OH-1004 89.241 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G255280

Location Chr01:64382995-64383750 (+)

Description Similar to VPS35B: Vacuolar protein sorting-associated protein 35B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g75850`	Plays a role in vesicular protein sorting.	Arabidopsis VPS35, a retromer component, is required for vacuolar protein sorting and involved in plant growth and leaf senescence.2008 · DOI: 10.1093/pcp/pcn006
`At2g17790`	Plays a role in vesicular protein sorting.	Loss-of-function mutations of retromer large subunit genes suppress the phenotype of an Arabidopsis zig mutant that lacks Qb-SNARE VTI11.2010 · DOI: 10.1105/tpc.109.069294
`At3g51310`	Plays a role in vesicular protein sorting.	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_015068 · 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:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0045053 protein retention in Golgi apparatus Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005768 endosome Cellular Component

GO:0005770 late endosome Cellular Component

GO:0005771 multivesicular body Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0010008 endosome membrane Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT1G75850

ath:AT2G17790

ath:AT3G51310

ddi:DDB_G0293218

mgr:MGG_05089

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.

Cytoplasm0.500

Rank 1 · TkA01G255280 · TK1151

Nucleus0.451

Rank 2 · TkA01G255280 · TK1151

Cell membrane0.100

Rank 3 · TkA01G255280 · TK1151

Mitochondrion0.063

Rank 4 · TkA01G255280 · TK1151

Endoplasmic reticulum0.053

Rank 5 · TkA01G255280 · 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.

PF03635Vps351-60 aa

PF26019HTH_TIMELESS5-26 aa

PF13910EMARD_N39-105 aa

PF15460SAS445-82 aa

PF26019HTH_TIMELESS55-79 aa

PF03635Vps3561-109 aa

PF15460SAS486-129 aa

PF26019HTH_TIMELESS100-110 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G255280	`PF03635`	Vps35	1	60	9.8e-41	140.8
TkA01G255280	`PF26019`	HTH_TIMELESS	5	26	0.048	14.6
TkA01G255280	`PF13910`	EMARD_N	39	105	0.12	12.0
TkA01G255280	`PF15460`	SAS4	45	82	0.14	13.0
TkA01G255280	`PF26019`	HTH_TIMELESS	55	79	0.048	14.6
TkA01G255280	`PF03635`	Vps35	61	109	9.8e-41	140.8
TkA01G255280	`PF15460`	SAS4	86	129	0.14	13.0
TkA01G255280	`PF26019`	HTH_TIMELESS	100	110	0.048	14.6

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
`F4I0P8`	Arabidopsis thaliana	sp\|F4I0P8\|VP35B_ARATH Vacuolar protein sorting-associated protein 35B	57.000%	Swiss-Prot	High
`Q7X659`	Arabidopsis thaliana	sp\|Q7X659\|VP35A_ARATH Vacuolar protein sorting-associated protein 35A	57.000%	Swiss-Prot	High
`A8R7K9`	Arabidopsis thaliana	sp\|A8R7K9\|VP35C_ARATH Vacuolar protein sorting-associated protein 35C	51.700%	Swiss-Prot	High

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