TkA06G047450 | RubberDandelionOmics

Gene overview

TkA06G047450

Reference: TK1151 Chr: Chr06 Coordinates: 12853111-12856777 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2145 bp · TkA06G047450|TK1151|cDNA

TCCATATCTCCCAGCCTACTCGTTCTCTAAAACCCTAATACTTTCTCTTCTAGGGTTTTTGTAGTTGCTCATTCCCGCAGCTACATCGAGACCTGCCTCCCTCTCTTAAGAACCCTACTTTGATTTCTCTTCTATTCTATTATTCTTATGGGGAAATCAGCTAAGAAATCTGCCTCCAAGGTTGAGTCAGCTACTGCTGTCGTAGCGCCCACCAAATCAATGAAAAAAGGCAAGAGAGACGCCGAGGAGATTGTCGTGAA...

CDS

Download CDS FASTA

1881 bp · TkA06G047450|TK1151|CDS

ATGGGGAAATCAGCTAAGAAATCTGCCTCCAAGGTTGAGTCAGCTACTGCTGTCGTAGCGCCCACCAAATCAATGAAAAAAGGCAAGAGAGACGCCGAGGAGATTGTCGTGAAGGAAGTAGTGAGTAGCAAGAAGCAGAAGGTAGTCAACGGTGCTGTTACTCAGGCTATTGAGAAGAAGAAGGTCGAGACTAAAACCCAAAAGAAGAACGTCAAGAAGCAAGAAAGCAGTTCTTCTGAAGAAGACTCAGACTCTGATGA...

Protein

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626 aa · TkA06G047450|TK1151|PROTEIN

MGKSAKKSASKVESATAVVAPTKSMKKGKRDAEEIVVKEVVSSKKQKVVNGAVTQAIEKKKVETKTQKKNVKKQESSSSEEDSDSDEEPKKVVAPAKKAAPVAKKPVKESSSDDSDSSSDEEPQPKKQSAPAAKKVPITKPESSSDESESDDSDSSDDEEAKKPAVPAKNGAVAAKKAESSDESDSDDSSDEEDAKAAKKPAVVKNGAGATPAKKAESSDDSSSEESDSEEEVKAAPAAKKPAPVAAAKKAESSDESSEE...

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	`TkA06G047450`
TK1151 ID	TkA06G047450
OH-1004 ID	LXL04_025648
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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Basic Information and Functional Annotation

Gene ID TkA06G047450

Location Chr06:12853111-12856777 (+)

Description Similar to NUCL2: Nucleolin 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18610`	Involved in pre-rRNA processing and ribosome assembly.	No verified direct reference in this release
`At1g48920`	Involved in pre-rRNA processing and ribosome assembly.	Arabidopsis nucleolin affects plant development and patterning.2007 · DOI: 10.1104/pp.106.093575
`At4g34110`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0620700`	Involved in pre-rRNA processing and ribosome assembly.	No verified direct reference in this release
`Os08g0192900`	Involved in pre-rRNA processing and ribosome assembly.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025648 · 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:0006351 DNA-templated transcription Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010305 leaf vascular tissue pattern formation Biological Process

GO:0010588 cotyledon vascular tissue pattern formation Biological Process

GO:0042254 ribosome biogenesis Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0048024 regulation of mRNA splicing, via spliceosome Biological Process

GO:0048364 root development Biological Process

GO:0048366 leaf development Biological Process

GO:0048367 shoot system development Biological Process

KEGG gene cross-reference

ath:AT1G48920

ath:AT3G18610

dosa:Os04g0620700

dosa:Os08g0192900

hsa:55147

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.

Nucleus0.936

Rank 1 · TkA06G047450 · TK1151

Cytoplasm0.167

Rank 2 · TkA06G047450 · TK1151

Extracellular0.032

Rank 3 · TkA06G047450 · TK1151

Cell membrane0.025

Rank 4 · TkA06G047450 · TK1151

Mitochondrion0.018

Rank 5 · TkA06G047450 · 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.

PF00076RRM_1369-436 aa

PF14605Nup35_RRM_2381-423 aa

PF24475RBD_DEAH11405-433 aa

PF14605Nup35_RRM_2463-524 aa

PF00076RRM_1480-536 aa

PF24475RBD_DEAH11512-540 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G047450	`PF00076`	RRM_1	369	436	8.2e-27	93.6
TkA06G047450	`PF14605`	Nup35_RRM_2	381	423	6e-05	23.6
TkA06G047450	`PF24475`	RBD_DEAH11	405	433	0.004	18.0
TkA06G047450	`PF14605`	Nup35_RRM_2	463	524	6e-05	23.6
TkA06G047450	`PF00076`	RRM_1	480	536	8.2e-27	93.6
TkA06G047450	`PF24475`	RBD_DEAH11	512	540	0.004	18.0

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
`Q1PEP5`	Arabidopsis thaliana	sp\|Q1PEP5\|NUCL2_ARATH Nucleolin 2	47.000%	Swiss-Prot	Low
`Q9FVQ1`	Arabidopsis thaliana	sp\|Q9FVQ1\|NUCL1_ARATH Nucleolin 1	48.600%	Swiss-Prot	Low
`P42731`	Arabidopsis thaliana	sp\|P42731\|PABP2_ARATH Polyadenylate-binding protein 2	30.400%	Swiss-Prot	Low
`Q7XTT4`	Oryza sativa subsp. japonica	sp\|Q7XTT4\|NUCL2_ORYSJ Nucleolin 2	52.100%	Swiss-Prot	Low
`Q6Z1C0`	Oryza sativa subsp. japonica	sp\|Q6Z1C0\|NUCL1_ORYSJ Nucleolin 1	50.300%	Swiss-Prot	Low

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