TkA01G552560 | RubberDandelionOmics

Gene overview

TkA01G552560

Reference: TK1151 Chr: Chr01 Coordinates: 138855088-138858853 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2493 bp · TkA01G552560|TK1151|cDNA

TAGTGTTGCCACTTAAAAGTGATTCTTCTCTTGGTTACCTCCATTTTTCGCAAGCCTTTCGCCGTCTTCTACTATTACCCAACAAGTCTCCCTTTTCTCCATATACTTTCACCAATTTCGAGAAATTGACAACCAGTCAGACCTGGAAAGCAACTGGTTCTTCAAGATCAATACTTAAACTGACACCCATTTCGATTATCGGCCTCTGTAAACAGCGAAACTAGAAGATTACATCAAATCACAAGTGCCTTACTGCATGA...

CDS

Download CDS FASTA

1689 bp · TkA01G552560|TK1151|CDS

ATGCCACTTTCAGAATTCTACGGATCTGTTAACGGAAAGAATGAATCCTCTCAGAAAAAGTCAACCGATATTTCATACATTCCAAATGACGAATTTGTGGAATTGGTATGGGAAAAGGGTCAAATCATGATGCAGGGTCAATCCAGTAAAGTTAGAAAAACGCCGGTTTCCAGTAATTTTCTTTTTCATACTCCAAAAGTTCAAGAAAAAGAAGTTCTTCTCGATGTACCTATGCAAGAACTTGATGACGACATGGTTCC...

Protein

Download Protein FASTA

562 aa · TkA01G552560|TK1151|PROTEIN

MPLSEFYGSVNGKNESSQKKSTDISYIPNDEFVELVWEKGQIMMQGQSSKVRKTPVSSNFLFHTPKVQEKEVLLDVPMQELDDDMVPWLNYPIDDYCSDLLPEISGVTGNDHNTFNALDKRSSYNHSNKDSHPPNVPRSSHVMDPSLRSGVSDIGNSNFRSKPQILEKLVQKQDSLPPYTSSPLLNFSHFSRPAAKAKANLQNHGPQKESGFAGRPSLDVSKVGSNRFVCKPVEEPRCVEKSSNNVVVDVNVGKGGGVEM...

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	`TkA01G552560`
TK1151 ID	TkA01G552560
OH-1004 ID	LXL04_001236
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 99.288 / OH-1004 81.698 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 TkA01G552560

Location Chr01:138855088-138858853 (+)

Description Similar to PIF3: Transcription factor PIF3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g09530`	Transcription factor acting in the phytochrome signaling pathway.	PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings.2013 · DOI: 10.1105/tpc.113.109710 Coordinated Regulation of Hypocotyl Cell Elongation by Light and Ethylene through a Microtubule Destabilizing Protein.2018 · DOI: 10.1104/pp.17.01109 Submergence stress-induced hypocotyl elongation through ethylene signaling-mediated regulation of cortical microtubules in Arabidopsis.2020 · DOI: 10.1093/jxb/erz453 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis.2020 · DOI: 10.1105/tpc.19.00515
`At2g20180`	Transcription activator.	SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5.2008 · DOI: 10.1105/tpc.108.058859

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0286100`	Transcription factor that may act as negative regulator of phyB-dependent light signal transduction.	Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa.2007 · DOI: 10.1271/bbb.60643
`Os05g0139100`	Atypical bHLH transcription factor that acts as a negative regulator of grain size.	No verified direct reference in this release
`Os03g0782500`	Transcription factor that may act as negative regulator of phyB-dependent light signal transduction.	Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa.2007 · DOI: 10.1271/bbb.60643 Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress.2012 · DOI: 10.1073/pnas.1207324109

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001236 · 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:0007165 signal transduction Biological Process

GO:0009408 response to heat Biological Process

GO:0009409 response to cold Biological Process

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

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

GO:0009641 shade avoidance Biological Process

GO:0009704 de-etiolation Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009733 response to auxin Biological Process

GO:0009737 response to abscisic acid Biological Process

KEGG gene cross-reference

ath:AT1G09530

ath:AT2G46970

dosa:Os01g0286100

dosa:Os03g0782500

dosa:Os05g0139100

osa:4327916

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.

Nucleus0.981

Rank 1 · TkA01G552560 · TK1151

Cytoplasm0.085

Rank 2 · TkA01G552560 · TK1151

Cell membrane0.021

Rank 3 · TkA01G552560 · TK1151

Endoplasmic reticulum0.011

Rank 4 · TkA01G552560 · TK1151

Plastid0.008

Rank 5 · TkA01G552560 · 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.

PF07555NAGidase80-101 aa

PF15374CCDC71L238-351 aa

PF07555NAGidase297-393 aa

PF00010HLH333-380 aa

PF23173bHLH_SAC51338-382 aa

PF23177bHLH_IRO3338-385 aa

PF23183bHLH_NPAS4340-360 aa

PF23176bHLH_LHW341-380 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G552560	`PF07555`	NAGidase	80	101	0.27	11.3
TkA01G552560	`PF15374`	CCDC71L	238	351	0.096	12.6
TkA01G552560	`PF07555`	NAGidase	297	393	0.27	11.3
TkA01G552560	`PF00010`	HLH	333	380	3.8e-14	52.9
TkA01G552560	`PF23173`	bHLH_SAC51	338	382	8.1e-08	32.8
TkA01G552560	`PF23177`	bHLH_IRO3	338	385	6.8e-05	23.9
TkA01G552560	`PF23183`	bHLH_NPAS4	340	360	1.6	9.4
TkA01G552560	`PF23176`	bHLH_LHW	341	380	0.011	16.4

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
`O80536`	Arabidopsis thaliana	sp\|O80536\|PIF3_ARATH Transcription factor PIF3	39.400%	Swiss-Prot	Medium
`Q8GZM7`	Arabidopsis thaliana	sp\|Q8GZM7\|PIF1_ARATH Transcription factor PIF1	33.200%	Swiss-Prot	Medium
`Q0JNI9`	Oryza sativa subsp. japonica	sp\|Q0JNI9\|PIL15_ORYSJ Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 15	46.100%	Swiss-Prot	Low
`Q6AT90`	Oryza sativa subsp. japonica	sp\|Q6AT90\|APG_ORYSJ Transcription factor APG	62.600%	Swiss-Prot	Low
`Q10CH5`	Oryza sativa subsp. japonica	sp\|Q10CH5\|PIL13_ORYSJ Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13	64.900%	Swiss-Prot	Low

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