TkA04G126470 | RubberDandelionOmics

Gene overview

TkA04G126470

Reference: TK1151 Chr: Chr04 Coordinates: 32835835-32843736 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4504 bp · TkA04G126470|TK1151|cDNA

GAAAAAGCAGACCATATTCGAAACTTGAATAAAATCCAAAGGGAATCGCTGTGACAAATGCGCGTAGAACAGTTTTAAGATGAAACCCTTTTCTATAAAAGCCATTCCAATGTGAAAAAACCCATTCAACTTCCTCTCTCTCATAATCATCTAAAACCCTGAATTATTCTACTTCAGTTCTTGCGTCTTTGCGTTTTCTATTATTTATTTCATCATTCCCCCTGTTTTGGTTGAAGATTCACAGCGGGAAACAGGATGGC...

CDS

Download CDS FASTA

4218 bp · TkA04G126470|TK1151|CDS

ATGGCCGCCAATGAAGATGGAAGCAATGGCGAAACATCTGCCTGCCATCTTCCGTTCGCGAGAAGTTATCAAATCGATGCCCTGGAGCAAGCGATAAAGCAGAACACAATAGTGTTCTTGGAGACCGGTGCCGGCAAAACGTTGATCGCCATCATGCTTCTACGCTACTATGCTTATCTGTTACGAAAACCATCACCTTTTTTCGCAGTTTTTTTGGTTCCCACTGTTGTCTTAGTCAAACAGCAAGCTGAAAACGTGAG...

Protein

Download Protein FASTA

1405 aa · TkA04G126470|TK1151|PROTEIN

MAANEDGSNGETSACHLPFARSYQIDALEQAIKQNTIVFLETGAGKTLIAIMLLRYYAYLLRKPSPFFAVFLVPTVVLVKQQAENVRKHVDLKVEEYWGDKGVDNWDASVWKKQQDENQVMVMTPQILLDALRHSFLSLDTIKLIIFDECHHAKKKHAMALIMKEFYHRNLREGGSELPRILGMTASPVEAKVSNSGNDYWEQISNLENQLNSKVYTCASESVLAGYIPFSTVKIEFYEDKELPYSILEGLKTNLSILRE...

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	`TkA04G126470`
TK1151 ID	TkA04G126470
OH-1004 ID	LXL04_002782
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	32.600
Protein coverage (%)	TK1151 98.292 / OH-1004 85.409 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 TkA04G126470

Location Chr04:32835835-32843736 (+)

Description Similar to DCL4: Dicer-like protein 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g03300`	Ribonuclease (RNase) III involved in RNA-mediated post-transcriptional gene silencing (PTGS).	No verified direct reference in this release
`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
`Os03g0583900`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os09g0315100`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os04g0509300`	Involved in the RNA silencing pathway.	The small interfering RNA production pathway is required for shoot meristem initiation in rice.2007 · DOI: 10.1073/pnas.0704339104 Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development.2007 · DOI: 10.1105/tpc.107.052209

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002782 · 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:0006353 DNA-templated transcription termination Biological Process

GO:0006995 cellular response to nitrogen starvation Biological Process

GO:0009616 RNAi-mediated antiviral immune response Biological Process

GO:0009944 polarity specification of adaxial/abaxial axis Biological Process

GO:0010050 vegetative phase change Biological Process

GO:0010267 ta-siRNA processing Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

GO:0010599 lsiRNA processing Biological Process

GO:0030422 siRNA processing Biological Process

GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation Biological Process

GO:0048608 reproductive structure development Biological Process

GO:0051214 RNAi-mediated antiviral immunity against RNA virus Biological Process

KEGG gene cross-reference

ath:AT3G03300

ath:AT5G20320

dosa:Os01g0909200

dosa:Os04g0509300

dosa:Os10g0485600

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.

Nucleus0.584

Rank 1 · TkA04G126470 · TK1151

Cytoplasm0.442

Rank 2 · TkA04G126470 · TK1151

Mitochondrion0.059

Rank 3 · TkA04G126470 · TK1151

Cell membrane0.045

Rank 4 · TkA04G126470 · TK1151

Endoplasmic reticulum0.031

Rank 5 · TkA04G126470 · 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.

PF04851ResIII21-188 aa

PF00270DEAD22-189 aa

PF00176SNF2-rel_dom30-160 aa

PF13401AAA_2236-161 aa

PF00176SNF2-rel_dom233-277 aa

PF14622Ribonucleas_3_3257-286 aa

PF00271Helicase_C374-486 aa

PF22590Cas3-like_C_2387-486 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G126470	`PF04851`	ResIII	21	188	1.8e-18	67.7
TkA04G126470	`PF00270`	DEAD	22	189	6.5e-18	65.7
TkA04G126470	`PF00176`	SNF2-rel_dom	30	160	1.8e-05	24.7
TkA04G126470	`PF13401`	AAA_22	36	161	0.016	16.3
TkA04G126470	`PF00176`	SNF2-rel_dom	233	277	1.8e-05	24.7
TkA04G126470	`PF14622`	Ribonucleas_3_3	257	286	1.5e-23	84.1
TkA04G126470	`PF00271`	Helicase_C	374	486	3.8e-15	56.8
TkA04G126470	`PF22590`	Cas3-like_C_2	387	486	0.0053	17.7
TkA04G126470	`PF03368`	Dicer_dimer	557	639	4.3e-16	59.4
TkA04G126470	`PF02170`	PAZ	656	666	1.5e-09	38.6
TkA04G126470	`PF02170`	PAZ	838	956	1.5e-09	38.6
TkA04G126470	`PF14622`	Ribonucleas_3_3	1004	1132	1.5e-23	84.1
TkA04G126470	`PF00636`	Ribonuclease_3	1006	1123	7.9e-43	146.1
TkA04G126470	`PF14622`	Ribonucleas_3_3	1173	1310	1.5e-23	84.1
TkA04G126470	`PF00636`	Ribonuclease_3	1196	1307	7.9e-43	146.1
TkA04G126470	`PF24999`	LAMB4	1246	1274	0.15	12.6

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q3EBC8`	Arabidopsis thaliana	sp\|Q3EBC8\|DCL2_ARATH Endoribonuclease Dicer homolog 2	52.400%	Swiss-Prot	High
`Q9SP32`	Arabidopsis thaliana	sp\|Q9SP32\|DCL1_ARATH Endoribonuclease Dicer homolog 1	32.300%	Swiss-Prot	Medium
`Q10HL3`	Oryza sativa subsp. japonica	sp\|Q10HL3\|DCL2A_ORYSJ Endoribonuclease Dicer homolog 2a	44.500%	Swiss-Prot	Medium
`Q69LX2`	Oryza sativa subsp. japonica	sp\|Q69LX2\|DCL2B_ORYSJ Endoribonuclease Dicer homolog 2b	43.400%	Swiss-Prot	Medium
`A7LFZ6`	Oryza sativa subsp. japonica	sp\|A7LFZ6\|DCL4_ORYSJ Endoribonuclease Dicer homolog 4	32.800%	Swiss-Prot	Medium

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