TkA01G611100 | RubberDandelionOmics

Gene overview

TkA01G611100

Reference: TK1151 Chr: Chr01 Coordinates: 154075851-154078744 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1684 bp · TkA01G611100|TK1151|cDNA

GTTTAATCTGAATAAAAAAACAAAATCACACGAAAACCCATTTATCTTAGAATTAGAAAGAGAAATCTTGCGACTTTCATCGATTTTGTCTAAGAACTTGCGGTTACAGCAAATGCTTAACGATCATCGTCAGGGTTGAAGCAACATAGCCGTACTCTTCCTTATCATAGCGATCGGACTTTCTACTCTGAACGAATTCAATCAGTTTCAGACCAAATCTCTTCCACTGACATCCGATTGCAACAAAAATCATGATCACA...

CDS

Download CDS FASTA

1215 bp · TkA01G611100|TK1151|CDS

ATGATCACAACGCAAAGAAGTCCTACAGGAGGAGGGGGTTTACAGAGCCCTAGATCCCCATCTTCGCAACCTCCGTTTCTGTCAGTATCTGTAACTGATCCTGCTAAAATGGGCAATGGAGTTCAAGCTTATATCTCCTATAAGGTCATCACCAAGACAAACTTTCCCGACTATCAAGGTCCAGAAAAGATTGTCATTCGCCGTTATACTGATTTTGTTTGGTTACGAGATTGTCTCTTCAAAAAGTACAAGGGCATCTT...

Protein

Download Protein FASTA

404 aa · TkA01G611100|TK1151|PROTEIN

MITTQRSPTGGGGLQSPRSPSSQPPFLSVSVTDPAKMGNGVQAYISYKVITKTNFPDYQGPEKIVIRRYTDFVWLRDCLFKKYKGIFIPPLPEKSTVEKFRFSAEFIEMRRQALDSFVNRIALHHELQHSEDLRTFLQADEQTMERARSQDTGIFKKKPSDFMQIFWDVQSKVSDVVLGKEKPVEETNPEYEKLKRYIFELEDHLAEAQKHAYRLVKRHRELGQSLGDFGKAIKLLGACEGDALGTAFSELGAKSEMLSV...

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	`TkA01G611100`
TK1151 ID	TkA01G611100
OH-1004 ID	LXL04_000451
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 99.010 / OH-1004 99.502 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 TkA01G611100

Location Chr01:154075851-154078744 (+)

Description Similar to SNX1: Sorting nexin 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g06140`	Plays a role in vesicular protein sorting.	AtSNX1 defines an endosome for auxin-carrier trafficking in Arabidopsis.2006 · DOI: 10.1038/nature05046 Evidence for a sorting endosome in Arabidopsis root cells.2008 · DOI: 10.1111/j.1365-313x.2007.03338.x Differential degradation of PIN2 auxin efflux carrier by retromer-dependent vacuolar targeting.2008 · DOI: 10.1073/pnas.0808073105 BLOS1, a putative BLOC-1 subunit, interacts with SNX1 and modulates root growth in Arabidopsis.2010 · DOI: 10.1242/jcs.069732 Analyses of sorting nexins reveal distinct retromer-subcomplex functions in development and protein sorting in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.078451

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000451 · 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:0006623 protein targeting to vacuole Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006896 Golgi to vacuole transport Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0031623 receptor internalization Biological Process

GO:0034498 early endosome to Golgi transport Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0045732 positive regulation of protein catabolic process Biological Process

GO:0048364 root development Biological Process

GO:0072659 protein localization to plasma membrane Biological Process

GO:0072673 lamellipodium morphogenesis Biological Process

KEGG gene cross-reference

ath:AT5G06140

bta:512029

hsa:6642

mmu:67804

pon:100174193

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.

Cytoplasm0.672

Rank 1 · TkA01G611100 · TK1151

Cell membrane0.285

Rank 2 · TkA01G611100 · TK1151

Golgi apparatus0.183

Rank 3 · TkA01G611100 · TK1151

Nucleus0.138

Rank 4 · TkA01G611100 · TK1151

Lysosome / Vacuole0.079

Rank 5 · TkA01G611100 · 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.

PF00787PX62-139 aa

PF02601Exonuc_VII_L109-158 aa

PF15754SPESP1119-198 aa

PF13870CCDC113_CCDC96_CC124-141 aa

PF09325Vps5181-394 aa

PF08663HalX186-207 aa

PF13870CCDC113_CCDC96_CC186-230 aa

PF10456BAR_3_WASP_bdg195-390 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G611100	`PF00787`	PX	62	139	1.5e-21	77.5
TkA01G611100	`PF02601`	Exonuc_VII_L	109	158	8.3	6.5
TkA01G611100	`PF15754`	SPESP1	119	198	0.096	12.6
TkA01G611100	`PF13870`	CCDC113_CCDC96_CC	124	141	7.6	6.9
TkA01G611100	`PF09325`	Vps5	181	394	1.8e-22	80.8
TkA01G611100	`PF08663`	HalX	186	207	0.39	11.8
TkA01G611100	`PF13870`	CCDC113_CCDC96_CC	186	230	7.6	6.9
TkA01G611100	`PF10456`	BAR_3_WASP_bdg	195	390	0.0041	17.3
TkA01G611100	`PF02601`	Exonuc_VII_L	249	363	8.3	6.5
TkA01G611100	`PF13870`	CCDC113_CCDC96_CC	303	364	7.6	6.9
TkA01G611100	`PF08663`	HalX	320	356	0.39	11.8

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
`Q9FG38`	Arabidopsis thaliana	sp\|Q9FG38\|SNX1_ARATH Sorting nexin 1	76.000%	Swiss-Prot	High

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