TkA01G361900 | RubberDandelionOmics

Gene overview

TkA01G361900

Reference: TK1151 Chr: Chr01 Coordinates: 89935278-89936889 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

471 bp · TkA01G361900|TK1151|cDNA

ATGAGCCCCCACTCTAATTTGACACCTAGAGAGTATCAATTAGATGTGTTTCAAGTGGCTATGCGGCGAAATACCATAGCTCATCTGGACACTGATGCCGGGAAAACAATGATAGCCATCCTAATCATCAAACAAGTATACTATGATCAAATCGCTGATTTTGCTATCACTACTGGCGTTAAGTTTGTTACGAAATCCAAATCAATTTTGCAAATAACTCTTATGGATTTTCAATTGCAGCAATTCAAGGTTCTAAAGGA...

CDS

Download CDS FASTA

471 bp · TkA01G361900|TK1151|CDS

ATGAGCCCCCACTCTAATTTGACACCTAGAGAGTATCAATTAGATGTGTTTCAAGTGGCTATGCGGCGAAATACCATAGCTCATCTGGACACTGATGCCGGGAAAACAATGATAGCCATCCTAATCATCAAACAAGTATACTATGATCAAATCGCTGATTTTGCTATCACTACTGGCGTTAAGTTTGTTACGAAATCCAAATCAATTTTGCAAATAACTCTTATGGATTTTCAATTGCAGCAATTCAAGGTTCTAAAGGA...

Protein

Download Protein FASTA

156 aa · TkA01G361900|TK1151|PROTEIN

MSPHSNLTPREYQLDVFQVAMRRNTIAHLDTDAGKTMIAILIIKQVYYDQIADFAITTGVKFVTKSKSILQITLMDFQLQQFKVLKENTDLTVDFYHGTKVGTMNGKKCLSCGKEFQDDGDMALKIKCKCQAEVGVGWHTDGERLHEICIKSLPHW

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	`TkA01G361900`
TK1151 ID	TkA01G361900
OH-1004 ID	LXL04_003426
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 94.545 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 TkA01G361900

Location Chr01:89935278-89936889 (-)

Description Similar to DCL3A: Endoribonuclease Dicer homolog 3a

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g01040`	Ribonuclease (RNase) III involved in RNA-mediated post- transcriptional gene silencing (PTGS).	Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana.2005 · DOI: 10.1007/s11103-004-6853-5 Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs.2005 · DOI: 10.1016/j.cub.2005.07.024 The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis.2006 · DOI: 10.1261/rna.2146906 A novel class of bacteria-induced small RNAs in Arabidopsis.2007 · DOI: 10.1101/gad.1595107 The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1.2008 · DOI: 10.1073/pnas.0803356105 Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1.2008 · DOI: 10.1073/pnas.0805760105

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0909200`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os10g0485600`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os03g0121800`	Involved in the RNA silencing pathway.	Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice.2005 · DOI: 10.1104/pp.105.063420 Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).2008 · DOI: 10.1073/pnas.0708743105

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003426 · 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:0010267 ta-siRNA processing Biological Process

GO:0030422 siRNA processing Biological Process

GO:0050688 regulation of defense response to virus Biological Process

GO:0051607 defense response to virus Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0004386 helicase activity Molecular Function

GO:0004525 ribonuclease III activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

act:ACLA_014840

afm:AFUA_5G11790

dosa:Os01g0909200

osa:4324864

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.

Nucleus0.620

Rank 1 · TkA01G361900 · TK1151

Cytoplasm0.342

Rank 2 · TkA01G361900 · TK1151

Extracellular0.062

Rank 3 · TkA01G361900 · TK1151

Mitochondrion0.045

Rank 4 · TkA01G361900 · TK1151

Endoplasmic reticulum0.034

Rank 5 · TkA01G361900 · 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.

PF04851ResIII8-79 aa

PF00270DEAD11-61 aa

PF30985OEP2125-130 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G361900	`PF04851`	ResIII	8	79	0.0088	16.7
TkA01G361900	`PF00270`	DEAD	11	61	0.069	13.6
TkA01G361900	`PF30985`	OEP21	25	130	0.025	15.7

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
`Q9SP32`	Arabidopsis thaliana	sp\|Q9SP32\|DCL1_ARATH Endoribonuclease Dicer homolog 1	38.200%	Swiss-Prot	Medium
`Q5N870`	Oryza sativa subsp. japonica	sp\|Q5N870\|DCL3A_ORYSJ Endoribonuclease Dicer homolog 3a	45.300%	Swiss-Prot	Medium
`Q7XD96`	Oryza sativa subsp. japonica	sp\|Q7XD96\|DCL3B_ORYSJ Endoribonuclease Dicer homolog 3b	37.300%	Swiss-Prot	Medium
`Q8LMR2`	Oryza sativa subsp. japonica	sp\|Q8LMR2\|DCL1_ORYSJ Endoribonuclease Dicer homolog 1	41.400%	Swiss-Prot	Low

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