TkA04G147720 | RubberDandelionOmics

Gene overview

TkA04G147720

Reference: TK1151 Chr: Chr04 Coordinates: 38265551-38266339 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

756 bp · TkA04G147720|TK1151|cDNA

ATGAAAAACTTCTCATCTGATCAAAACCACCCAAACCCACCACCAGATGATTCCGATCAACAGAACAGGTCGACACCGACGAAGTCTGAGTGGGACTTCCGCGTCTCCGCTGTGGTTTCATCCTCCGTTACCGGCGGACACATCTCGGACACTCTCGGCGTCGTAGAGGTTGACTCCTCCGGAAACCTCTTCGCTACCGGCGGTATTGCTAGGAAGATCCGAGTTTATAGCTTAAATTCCTTGCTATCATCAGAGTATTG...

CDS

Download CDS FASTA

756 bp · TkA04G147720|TK1151|CDS

ATGAAAAACTTCTCATCTGATCAAAACCACCCAAACCCACCACCAGATGATTCCGATCAACAGAACAGGTCGACACCGACGAAGTCTGAGTGGGACTTCCGCGTCTCCGCTGTGGTTTCATCCTCCGTTACCGGCGGACACATCTCGGACACTCTCGGCGTCGTAGAGGTTGACTCCTCCGGAAACCTCTTCGCTACCGGCGGTATTGCTAGGAAGATCCGAGTTTATAGCTTAAATTCCTTGCTATCATCAGAGTATTG...

Protein

Download Protein FASTA

251 aa · TkA04G147720|TK1151|PROTEIN

MKNFSSDQNHPNPPPDDSDQQNRSTPTKSEWDFRVSAVVSSSVTGGHISDTLGVVEVDSSGNLFATGGIARKIRVYSLNSLLSSEYCICTPAKLSSLKWKPGSAGRIMGSADYDGVVTEYDLETKMPVYERDEHNGRRVWSMDYSHWDPVVGASGADDGTMQMWDPRHDSEKCVAKVALGSPVCCVEFSPFGGALVAVGCADRKAYVYDVRKIVDPIAVFDGHGRTVSYTRFLDDHTVVTSGTDGCLKMWT

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	`TkA04G147720`
TK1151 ID	TkA04G147720
OH-1004 ID	LXL04_035273
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	95.400
Protein coverage (%)	TK1151 99.602 / OH-1004 71.117 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 TkA04G147720

Location Chr04:38265551-38266339 (+)

Description Similar to RUP2: WD repeat-containing protein RUP2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g52250`	Functions in association with RUP2 as repressor of UV-B-induced photomorphogenesis mediated by UVR8 and HY5, likely in coordination with DHU1.	Negative feedback regulation of UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.2010 · DOI: 10.1073/pnas.0914532107 EFO1 and EFO2, encoding putative WD-domain proteins, have overlapping and distinct roles in the regulation of vegetative development and flowering of Arabidopsis.2011 · DOI: 10.1093/jxb/erq336 DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1.2017 · DOI: 10.1016/j.bbrc.2017.07.110
`At5g23730`	Functions in association with RUP1 as repressor of UV-B-induced photomorphogenesis mediated by UVR8 and HY5.	Negative feedback regulation of UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis.2010 · DOI: 10.1073/pnas.0914532107 EFO1 and EFO2, encoding putative WD-domain proteins, have overlapping and distinct roles in the regulation of vegetative development and flowering of Arabidopsis.2011 · DOI: 10.1093/jxb/erq336
`At3g15354`	Repressor of photomorphogenesis in the light.	The SPA1-like proteins SPA3 and SPA4 repress photomorphogenesis in the light.2003 · DOI: 10.1046/j.1365-313x.2003.01813.x Functional and expression analysis of Arabidopsis SPA genes during seedling photomorphogenesis and adult growth.2006 · DOI: 10.1111/j.1365-313x.2006.02812.x Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability.2006 · DOI: 10.1242/dev.02481
`At2g32950`	E3 ubiquitin-protein ligase that acts as a repressor of photomorphogenesis and as an activator of etiolation in darkness.	Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis.2002 · DOI: 10.1101/gad.969702 Short Hypocotyl in White Light1 Interacts with Elongated Hypocotyl5 (HY5) and Constitutive Photomorphogenic1 (COP1) and Promotes COP1-Mediated Degradation of HY5 during Arabidopsis Seedling Development.2015 · DOI: 10.1104/pp.15.01184 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis.2020 · DOI: 10.1105/tpc.19.00515 Role of a COP1 interactive protein in mediating light-regulated gene expression in arabidopsis.1998 · DOI: 10.1105/tpc.10.7.1083
`At1g53090`	Repressor of photomorphogenesis in the light.	The SPA1-like proteins SPA3 and SPA4 repress photomorphogenesis in the light.2003 · DOI: 10.1046/j.1365-313x.2003.01813.x Functional and expression analysis of Arabidopsis SPA genes during seedling photomorphogenesis and adult growth.2006 · DOI: 10.1111/j.1365-313x.2006.02812.x Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability.2006 · DOI: 10.1242/dev.02481

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_035273 · 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:0009585 red, far-red light phototransduction Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009641 shade avoidance Biological Process

GO:0009647 skotomorphogenesis Biological Process

GO:0009649 entrainment of circadian clock Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009908 flower development Biological Process

GO:0009963 positive regulation of flavonoid biosynthetic process Biological Process

GO:0010114 response to red light Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0010218 response to far red light Biological Process

KEGG gene cross-reference

ath:AT2G32950

ath:AT3G15354

ath:AT5G23730

ath:AT5G52250

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.879

Rank 1 · TkA04G147720 · TK1151

Cytoplasm0.207

Rank 2 · TkA04G147720 · TK1151

Cell membrane0.026

Rank 3 · TkA04G147720 · TK1151

Mitochondrion0.017

Rank 4 · TkA04G147720 · TK1151

Lysosome / Vacuole0.017

Rank 5 · TkA04G147720 · 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.

PF25173Beta-prop_WDR3_1st31-175 aa

PF24814WD40_Prp1931-111 aa

PF00400WD4046-77 aa

PF25174Beta-prop_THOC346-82 aa

PF23414Beta-prop_EML_247-151 aa

PF24814WD40_Prp1949-250 aa

PF24817WD40_WDHD1_1st50-142 aa

PF25175Beta-prop_WDR552-189 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G147720	`PF25173`	Beta-prop_WDR3_1st	31	175	2.3e-14	54.2
TkA04G147720	`PF24814`	WD40_Prp19	31	111	4.5e-13	49.6
TkA04G147720	`PF00400`	WD40	46	77	8.9e-16	58.3
TkA04G147720	`PF25174`	Beta-prop_THOC3	46	82	1.3e-13	51.3
TkA04G147720	`PF23414`	Beta-prop_EML_2	47	151	5e-13	49.7
TkA04G147720	`PF24814`	WD40_Prp19	49	250	4.5e-13	49.6
TkA04G147720	`PF24817`	WD40_WDHD1_1st	50	142	1.6e-08	34.8
TkA04G147720	`PF25175`	Beta-prop_WDR5	52	189	1.2e-18	68.2
TkA04G147720	`PF24807`	WD40_CDC20-Fz	53	250	6.5e-15	55.9
TkA04G147720	`PF24782`	WD40_MABP1-WDR62_2nd	53	80	1.6e-07	31.3
TkA04G147720	`PF24805`	EIF3I	53	79	0.00021	21.2
TkA04G147720	`PF23760`	Beta-prop_DCAF12	53	81	0.0038	16.9
TkA04G147720	`PF23381`	Beta-prop_IFT122_1st	55	250	3.6e-13	50.2
TkA04G147720	`PF25172`	Beta-prop_WDR3_2nd	55	77	1.4e-05	25.2
TkA04G147720	`PF25168`	Beta-prop_WDR36-Utp21_2nd	55	214	2.2e-05	24.6
TkA04G147720	`PF17005`	WD40_like	55	82	0.037	14.1

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
`Q9LTJ6`	Arabidopsis thaliana	sp\|Q9LTJ6\|RUP1_ARATH WD repeat-containing protein RUP1	58.600%	Swiss-Prot	High
`Q9FFA7`	Arabidopsis thaliana	sp\|Q9FFA7\|RUP2_ARATH WD repeat-containing protein RUP2	58.800%	Swiss-Prot	High
`Q9LJR3`	Arabidopsis thaliana	sp\|Q9LJR3\|SPA3_ARATH Protein SPA1-RELATED 3	39.000%	Swiss-Prot	Medium
`P43254`	Arabidopsis thaliana	sp\|P43254\|COP1_ARATH E3 ubiquitin-protein ligase COP1	33.600%	Swiss-Prot	Medium
`Q94BM7`	Arabidopsis thaliana	sp\|Q94BM7\|SPA4_ARATH Protein SPA1-RELATED 4	36.000%	Swiss-Prot	Medium

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