TkA01G009860 | RubberDandelionOmics

Gene overview

TkA01G009860

Reference: TK1151 Chr: Chr01 Coordinates: 2689947-2696500 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2092 bp · TkA01G009860|TK1151|cDNA

TCAATTAAAATATGTACAAATATCCAAGTTCTGATGATAGAACGGTGTTTATTAGCTTCCTTCTCTTTTGTCTCGCCGCCGGTTGTATGCTAGCCTCTTTTATATTCCGGTTGCCTTTTTTCTCAACAACTCCTTCACTCTTCAACACCATAAATAGGAATCTCTTTAATACACGTACGCTTATACGAATTTCTAGGTCTCCATCAGTGGCGGACTTATCTCAGCAGCAGAATCTGCCGTCGTCGACCACCTGGTATTCG...

CDS

Download CDS FASTA

3069 bp · TkA01G009860|TK1151|CDS

ATGGAAGCAGACAACCAGTCCCAAATGGAGCTACCAAAACCCAATCCTGTACCTGTTCTTCCACCACGGGTACCCTTACGCCCTTTCCTCCTTTGGTGTTCTTCTTCAAACTCACTGATGAATCTCATTCTAAGGTATCCAGATTATTCAAAAAATCAAATAGATATACCAGAATCCCAACTCTTGATTCATTTCCCTAAGAACACAAGCTATCACCTACTTGACTTGGATAAGTATCATCCAAAAACTCCAGCTATTGG...

Protein

Download Protein FASTA

1022 aa · TkA01G009860|TK1151|PROTEIN

MEADNQSQMELPKPNPVPVLPPRVPLRPFLLWCSSSNSLMNLILRYPDYSKNQIDIPESQLLIHFPKNTSYHLLDLDKYHPKTPAIGAPVEIKASSHFNGFEVTHSCNGLLLLEHIKDDYHRAIVCNPLTGEYIFLPESTHVSKNAICAFFVSPSTHQFKVLRVFHRVAPPNPVPDSDSDSDRSMELDMSSHCSTELDPFSDSDIHSDESVLSSDYDYDSIFGSDSESTDPDDYSVDSDFDRMGEVLVSDSDSWESVIEP...

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	`TkA01G009860`
TK1151 ID	TkA01G009860
OH-1004 ID	LXL04_005880
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	96.100
Protein coverage (%)	TK1151 42.661 / OH-1004 93.737 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 TkA01G009860

Location Chr01:2689947-2696500 (-)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g12770`	Essential protein required during embryogenesis.	Identification of a developmental transition in plasmodesmatal function during embryogenesis in Arabidopsis thaliana.2002 · DOI: 10.1242/dev.129.5.1261 Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata.2009 · DOI: 10.1073/pnas.0909229106 Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata.2010 · DOI: 10.1016/j.cub.2010.03.064

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0636300`	DEAD-box ATP-dependent RNA helicase 47A.	No verified direct reference in this release
`Os03g0219700`	DEAD-box ATP-dependent RNA helicase 47B.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_005880 · 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) No functional description available

KEGG gene cross-reference No functional description available

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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.

Plastid0.642

Rank 1 · TkA01G009860 · TK1151

Nucleus0.173

Rank 2 · TkA01G009860 · TK1151

Cytoplasm0.126

Rank 3 · TkA01G009860 · TK1151

Mitochondrion0.102

Rank 4 · TkA01G009860 · TK1151

Cell membrane0.040

Rank 5 · TkA01G009860 · 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.

PF08268FBA_361-165 aa

PF07734FBA_174-172 aa

PF03478Beta-prop_KIB1-496-164 aa

PF07734FBA_1246-393 aa

PF08268FBA_3292-416 aa

PF03478Beta-prop_KIB1-4382-391 aa

PF00270DEAD602-798 aa

PF04851ResIII606-746 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G009860	`PF08268`	FBA_3	61	165	2.6e-13	50.4
TkA01G009860	`PF07734`	FBA_1	74	172	2.3e-16	60.4
TkA01G009860	`PF03478`	Beta-prop_KIB1-4	96	164	0.039	14.2
TkA01G009860	`PF07734`	FBA_1	246	393	2.3e-16	60.4
TkA01G009860	`PF08268`	FBA_3	292	416	2.6e-13	50.4
TkA01G009860	`PF03478`	Beta-prop_KIB1-4	382	391	0.039	14.2
TkA01G009860	`PF00270`	DEAD	602	798	5.6e-37	127.8
TkA01G009860	`PF04851`	ResIII	606	746	6.7e-05	23.6
TkA01G009860	`PF00271`	Helicase_C	870	978	3.8e-22	79.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8W4E1`	Arabidopsis thaliana	sp\|Q8W4E1\|RH47_ARATH DEAD-box ATP-dependent RNA helicase 47, mitochondrial	61.100%	Swiss-Prot	High
`Q6H874`	Oryza sativa subsp. japonica	sp\|Q6H874\|RH47A_ORYSJ DEAD-box ATP-dependent RNA helicase 47A	60.500%	Swiss-Prot	High
`Q10PV9`	Oryza sativa subsp. japonica	sp\|Q10PV9\|RH47B_ORYSJ DEAD-box ATP-dependent RNA helicase 47B	60.400%	Swiss-Prot	High

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