TkA07G421120 | RubberDandelionOmics

Gene overview

TkA07G421120

Reference: TK1151 Chr: Chr07 Coordinates: 106425402-106428248 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2064 bp · TkA07G421120|TK1151|cDNA

GATGTACTACTATGTACTGAATCAGCAAAAACTCCCCCTACTATTATCCCAAAATCATACACCTCAAATATCCATGGCCCACGTCTCGATGATGTGGAATCTCTACACGATGTTTTCATCTGGGGTGAAGGAACATGCGACAGACTGTTAGGCGGCGGAATCGGAATGTCTAATTCCAATTCCGCCAAAATCGATTCCCTTTCCCCAAAGGCATTAAAGCGAAGCATAGCTTTCGATGCAAGAAAAGTATCATGCGGAAG...

CDS

Download CDS FASTA

2046 bp · TkA07G421120|TK1151|CDS

GATGTACTACTATGTACTGAATCAGCAAAAACTCCCCCTACTATTATCCCAAAATCATACACCTCAAATATCCATGGCCCACGTCTCGATGATGTGGAATCTCTACACGATGTTTTCATCTGGGGTGAAGGAACATGCGACAGACTGTTAGGCGGCGGAATCGGAATGTCTAATTCCAATTCCGCCAAAATCGATTCCCTTTCCCCAAAGGCATTAAAGCGAAGCATAGCTTTCGATGCAAGAAAAGTATCATGCGGAAG...

Protein

Download Protein FASTA

681 aa · TkA07G421120|TK1151|PROTEIN

DVLLCTESAKTPPTIIPKSYTSNIHGPRLDDVESLHDVFIWGEGTCDRLLGGGIGMSNSNSAKIDSLSPKALKRSIAFDARKVSCGSKHAVLITKQGEVYSWGEGSGGRLGHGTESDIPIPKLIDDLSRSNIEMVACGENHTLALTQSGDVYTWGEIISPGTGTGIGISHWIPGKIGGPLEGINVKFISCGPWHSAIITSEGVLFTFGDGTFGALGHGDTATIYHPKPVQSLIDKKTVKVSCGFWHTAAIVQIDGSSSTK...

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	`TkA07G421120`
TK1151 ID	TkA07G421120
OH-1004 ID	LXL04_030647
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.300
Protein coverage (%)	TK1151 100.000 / OH-1004 79.837 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA07G421120

Location Chr07:106425402-106428248 (+)

Description Similar to PRAF1: PH, RCC1 and FYVE domains-containing protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g76950`	Binds to phosphatidic acid and to phosphoinositides such as PtdIns3P, PtdIns(3,4)P(2), PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2).	No verified direct reference in this release
`At5g63860`	UV-B specific signaling component that acts as a UV-B photoreceptor and plays a key role in establishing UV-protective responses in plants.	A UV-B-specific signaling component orchestrates plant UV protection.2005 · DOI: 10.1073/pnas.0507187102 UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus.2007 · DOI: 10.1105/tpc.107.053330 UV-B signaling pathways with different fluence-rate response profiles are distinguished in mature Arabidopsis leaf tissue by requirement for UVR8, HY5, and HYH.2008 · DOI: 10.1104/pp.107.108456 Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.2009 · DOI: 10.1038/emboj.2009.4 UVR8 in Arabidopsis thaliana regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation.2009 · DOI: 10.1111/j.1469-8137.2009.02855.x Negative feedback regulation of UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.2010 · DOI: 10.1073/pnas.0914532107 Functional interaction of the circadian clock and UV RESISTANCE LOCUS 8-controlled UV-B signaling pathways in Arabidopsis thaliana.2011 · DOI: 10.1111/j.1365-313x.2011.04573.x Perception of UV-B by the Arabidopsis UVR8 protein.2011 · DOI: 10.1126/science.1200660 UVR8 mediates UV-B-induced Arabidopsis defense responses against Botrytis cinerea by controlling sinapate accumulation.2012 · DOI: 10.1093/mp/sss025 C-terminal region of the UV-B photoreceptor UVR8 initiates signaling through interaction with the COP1 protein.2012 · DOI: 10.1073/pnas.1210898109 In vivo function of tryptophans in the Arabidopsis UV-B photoreceptor UVR8.2012 · DOI: 10.1105/tpc.112.101451 The UV-B photoreceptor UVR8 promotes photosynthetic efficiency in Arabidopsis thaliana exposed to elevated levels of UV-B.2012 · DOI: 10.1007/s11120-012-9785-y
`At5g60870`	Regulates DNA damage response (DDR) synergistically with ATM.	The RCC1 family protein RUG3 is required for splicing of nad2 and complex I biogenesis in mitochondria of Arabidopsis thaliana.2011 · DOI: 10.1111/j.1365-313x.2011.04658.x RUG3 and ATM synergistically regulate the alternative splicing of mitochondrial nad2 and the DNA damage response in Arabidopsis thaliana.2017 · DOI: 10.1038/srep43897 RUG3 is a negative regulator of plant responses to ABA in Arabidopsis thaliana.2017 · DOI: 10.1080/15592324.2017.1333217

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030647 · 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:0006281 DNA repair Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0009411 response to UV Biological Process

GO:0009649 entrainment of circadian clock Biological Process

GO:0010224 response to UV-B Biological Process

GO:0010374 stomatal complex development Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0045746 negative regulation of Notch signaling pathway Biological Process

GO:0050821 protein stabilization Biological Process

GO:0000785 chromatin Cellular Component

KEGG gene cross-reference

ath:AT1G76950

ath:AT5G63860

mmu:15204

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.

Cytoplasm0.539

Rank 1 · TkA07G421120 · TK1151

Nucleus0.299

Rank 2 · TkA07G421120 · TK1151

Cell membrane0.188

Rank 3 · TkA07G421120 · TK1151

Lysosome / Vacuole0.060

Rank 4 · TkA07G421120 · TK1151

Golgi apparatus0.058

Rank 5 · TkA07G421120 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF25390WD40_RLD37-399 aa

PF00415RCC137-93 aa

PF13540RCC1_237-46 aa

PF13540RCC1_281-106 aa

PF25384Alsin_RLD83-153 aa

PF07569Hira83-102 aa

PF00415RCC196-145 aa

PF07569Hira129-154 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G421120	`PF25390`	WD40_RLD	37	399	1.2e-78	265.7
TkA07G421120	`PF00415`	RCC1	37	93	5.1e-73	242.2
TkA07G421120	`PF13540`	RCC1_2	37	46	6.3e-43	144.3
TkA07G421120	`PF13540`	RCC1_2	81	106	6.3e-43	144.3
TkA07G421120	`PF25384`	Alsin_RLD	83	153	1.8e-12	47.8
TkA07G421120	`PF07569`	Hira	83	102	0.18	12.1
TkA07G421120	`PF00415`	RCC1	96	145	5.1e-73	242.2
TkA07G421120	`PF07569`	Hira	129	154	0.18	12.1
TkA07G421120	`PF13540`	RCC1_2	135	155	6.3e-43	144.3
TkA07G421120	`PF00415`	RCC1	148	198	5.1e-73	242.2
TkA07G421120	`PF13540`	RCC1_2	185	213	6.3e-43	144.3
TkA07G421120	`PF07569`	Hira	185	205	0.18	12.1
TkA07G421120	`PF00415`	RCC1	201	250	5.1e-73	242.2
TkA07G421120	`PF25384`	Alsin_RLD	204	321	1.8e-12	47.8
TkA07G421120	`PF13540`	RCC1_2	238	271	6.3e-43	144.3
TkA07G421120	`PF00415`	RCC1	261	307	5.1e-73	242.2

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
`Q947D2`	Arabidopsis thaliana	sp\|Q947D2\|PRAF1_ARATH PH, RCC1 and FYVE domains-containing protein 1	40.900%	Swiss-Prot	Medium
`Q9FN03`	Arabidopsis thaliana	sp\|Q9FN03\|UVR8_ARATH Ultraviolet-B receptor UVR8	34.100%	Swiss-Prot	Low
`Q9FJG9`	Arabidopsis thaliana	sp\|Q9FJG9\|RUG3_ARATH RCC1 domain-containing protein RUG3, mitochondrial	31.600%	Swiss-Prot	Low

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