TkA03G405200 | RubberDandelionOmics

Gene overview

TkA03G405200

Reference: TK1151 Chr: Chr03 Coordinates: 100764020-100769934 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1412 bp · TkA03G405200|TK1151|cDNA

TTTTAAGATGATTCTATGGTAAAACCAAAGGCGGATTCATTGGGAGGAGGCGGGACGCTTTCCCTCCAATCCATCACCCCCATTTTTGCTCTCATCAAGCTCAAGGAGTAGTCGTGATGTTTGATGATCGGTAACGGTTTAGGAAGAGATGTGAAAGCAGTTGTTACAGTATCTCCCGAACGATACTCGATTTCTCTGTGTTTAATCGCGAAATTGTGTAGAATTAAGTGACGAAGAGTCATAACTGAAGTGTGGAATGA...

CDS

Download CDS FASTA

1875 bp · TkA03G405200|TK1151|CDS

ATGGAACAGATCTCTCCAAAAAGCAACCATGAAAACAATTCACAACCAGAATCAGAATCCGAAAATGGAAAAAAGGAATTCGTTTCCCCTTCGGTAGGAATGGAATTCGAATCATACGATGACGCGTACAATTACTACAATTGTTACGCCCGCGAATCCGGATTTCGCGTACGTGTCAAAAACTCATGGTTCAAAAGAAACAGCCGAGAAAAATACGGCGCGGTTTTATGTTGCAGCAGTCAAGGCTTCAAAAGAATAAA...

Protein

Download Protein FASTA

624 aa · TkA03G405200|TK1151|PROTEIN

MEQISPKSNHENNSQPESESENGKKEFVSPSVGMEFESYDDAYNYYNCYARESGFRVRVKNSWFKRNSREKYGAVLCCSSQGFKRIKDVNRLRKETRTGCPAMVRMRLVDSRRWRILEVTLDHNHLLTTKSLKSLKKLGICGTKKSIQSDSETQTVKLYRALVIDSGGNHVNSRNTRELGSSSDYLPDRLNLKKGDSQAIYNYICRMQLTNPNFFYLMDVTDEGNLKNMIWLDARCRAAIGYFSDVVYFDTSYLSSKYEV...

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	`TkA03G405200`
TK1151 ID	TkA03G405200
OH-1004 ID	LXL04_009174
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.100
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 TkA03G405200

Location Chr03:100764020-100769934 (-)

Description Similar to FRS6: Protein FAR1-RELATED SEQUENCE 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g52520`	Putative transcription activator involved in regulating light control of development.	Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development.2004 · DOI: 10.1104/pp.104.052191
`At1g80010`	Putative transcription activator involved in regulating light control of development.	Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development.2004 · DOI: 10.1104/pp.104.052191
`At3g22170`	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'.	Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1.2002 · DOI: 10.1093/emboj/21.6.1339 The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway.2003 · DOI: 10.1046/j.1365-313x.2003.01741.x Arabidopsis FHY3 specifically gates phytochrome signaling to the circadian clock.2006 · DOI: 10.1105/tpc.105.037358 Transposase-derived transcription factors regulate light signaling in Arabidopsis.2007 · DOI: 10.1126/science.1146281 Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction.2008 · DOI: 10.1104/pp.108.120436 Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.2012 · DOI: 10.1105/tpc.112.097022
`At1g76320`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`At4g15090`	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009174 · 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:0006355 regulation of DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009639 response to red or far red light Biological Process

GO:0010017 red or far-red light signaling pathway Biological Process

GO:0010018 far-red light signaling pathway Biological Process

GO:0010218 response to far red light Biological Process

GO:0042753 positive regulation of circadian rhythm Biological Process

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

GO:1900056 negative regulation of leaf senescence Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G52520

ath:AT1G76320

ath:AT1G80010

ath:AT3G22170

ath:AT4G15090

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 · TkA03G405200 · TK1151

Cytoplasm0.090

Rank 2 · TkA03G405200 · TK1151

Cell membrane0.023

Rank 3 · TkA03G405200 · TK1151

Plastid0.015

Rank 4 · TkA03G405200 · TK1151

Endoplasmic reticulum0.013

Rank 5 · TkA03G405200 · 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.

PF03101FAR144-128 aa

PF24548EF_EFCAB10_C134-153 aa

PF24548EF_EFCAB10_C215-224 aa

PF21056ZSWIM1-3_RNaseH-like221-330 aa

PF10551MULE246-342 aa

PF03101FAR1452-479 aa

PF04434SWIM505-530 aa

PF24548EF_EFCAB10_C591-613 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G405200	`PF03101`	FAR1	44	128	2.1e-21	77.1
TkA03G405200	`PF24548`	EF_EFCAB10_C	134	153	0.0059	16.9
TkA03G405200	`PF24548`	EF_EFCAB10_C	215	224	0.0059	16.9
TkA03G405200	`PF21056`	ZSWIM1-3_RNaseH-like	221	330	0.023	15.3
TkA03G405200	`PF10551`	MULE	246	342	7.5e-25	87.9
TkA03G405200	`PF03101`	FAR1	452	479	2.1e-21	77.1
TkA03G405200	`PF04434`	SWIM	505	530	0.00019	21.6
TkA03G405200	`PF24548`	EF_EFCAB10_C	591	613	0.0059	16.9

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
`Q9SSQ4`	Arabidopsis thaliana	sp\|Q9SSQ4\|FRS6_ARATH Protein FAR1-RELATED SEQUENCE 6	60.400%	Swiss-Prot	High
`Q9S793`	Arabidopsis thaliana	sp\|Q9S793\|FRS8_ARATH Protein FAR1-RELATED SEQUENCE 8	43.200%	Swiss-Prot	Medium
`Q9LIE5`	Arabidopsis thaliana	sp\|Q9LIE5\|FHY3_ARATH Protein FAR-RED ELONGATED HYPOCOTYL 3	33.500%	Swiss-Prot	Medium
`Q6NQJ7`	Arabidopsis thaliana	sp\|Q6NQJ7\|FRS4_ARATH Protein FAR1-RELATED SEQUENCE 4	32.100%	Swiss-Prot	Medium
`Q9SWG3`	Arabidopsis thaliana	sp\|Q9SWG3\|FAR1_ARATH Protein FAR-RED IMPAIRED RESPONSE 1	31.600%	Swiss-Prot	Medium

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