LXL04_035273 | RubberDandelionOmics

Gene overview

LXL04_035273

Reference: OH-1004 Chr: Chr08 Coordinates: 18953724-18954827 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1104 bp · LXL04_035273|LXL04_035273|OH1004|cDNA

ATGAAAAACTTCTCATCTGATCAAAACCACCCAAACCCACCACCAGATGATTCCGATCAACAGAACAGGTCGACACCGACGAAGTCTGAGTGGGACTTCCGCGTCTCCGCTGTGGTTTCATCCTCCGTTACCGGCGGACACATCTCGGACACTCTCGGCGTCGTAGAGGTTGACTCCTCCGGAAACCTCTTCGCTTCCGGCGGTATTGCTAGGAAGATCCGAGTTTATAGCTTAAATTCCTTGCTATCATCAGAGGTAAC...

CDS

Download CDS FASTA

1104 bp · LXL04_035273|LXL04_035273|OH1004|CDS

ATGAAAAACTTCTCATCTGATCAAAACCACCCAAACCCACCACCAGATGATTCCGATCAACAGAACAGGTCGACACCGACGAAGTCTGAGTGGGACTTCCGCGTCTCCGCTGTGGTTTCATCCTCCGTTACCGGCGGACACATCTCGGACACTCTCGGCGTCGTAGAGGTTGACTCCTCCGGAAACCTCTTCGCTTCCGGCGGTATTGCTAGGAAGATCCGAGTTTATAGCTTAAATTCCTTGCTATCATCAGAGGTAAC...

Protein

Download Protein FASTA

367 aa · LXL04_035273|LXL04_035273|OH1004|PROTEIN

MKNFSSDQNHPNPPPDDSDQQNRSTPTKSEWDFRVSAVVSSSVTGGHISDTLGVVEVDSSGNLFASGGIARKIRVYSLNSLLSSEVTLLDHATALHYCICTPAKLSSLKWKPGSAGRIMGSADYDGVVTEYDLETKMPVYERDEHNGRRVWSMDYSHWDPVVGASGADDGTMQMWDPRHDSEKCVAKVALGSPVCCVEFSPFGGALVAVGCADRKAYVYDVRKIVDPIAVFDGHGRTVSYTRFLDDHTVVTSGTDGCLKM...

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	`LXL04_035273`
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_035273

Location Chr08:18953724-18954827 (-)

Description Similar to RUP2: WD repeat-containing protein RUP2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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
`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

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.

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.

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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.

Nucleus0.875

Rank 1 · LXL04_035273 · OH-1004

Cytoplasm0.207

Rank 2 · LXL04_035273 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_035273 · OH-1004

Mitochondrion0.018

Rank 4 · LXL04_035273 · OH-1004

Lysosome / Vacuole0.018

Rank 5 · LXL04_035273 · OH-1004

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.

PF25175.2Beta-prop_WDR552-307 aa

PF24782.3WD40_MABP1-WDR62_2nd56-262 aa

PF24807.2WD40_CDC20-Fz83-238 aa

PF23381.2Beta-prop_IFT122_1st102-222 aa

PF25174.2Beta-prop_THOC3104-306 aa

PF24814.2WD40_Prp19105-254 aa

PF29037.1DSE1_N107-182 aa

PF23414.2Beta-prop_EML_2119-249 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035273	`PF25175.2`	Beta-prop_WDR5	52	307	7.4e-26	91.8
LXL04_035273	`PF24782.3`	WD40_MABP1-WDR62_2nd	56	262	1.6e-11	44.5
LXL04_035273	`PF24807.2`	WD40_CDC20-Fz	83	238	4.2e-24	86.1
LXL04_035273	`PF23381.2`	Beta-prop_IFT122_1st	102	222	7.1e-19	68.9
LXL04_035273	`PF25174.2`	Beta-prop_THOC3	104	306	1.2e-24	87.6
LXL04_035273	`PF24814.2`	WD40_Prp19	105	254	1.4e-16	61.2
LXL04_035273	`PF29037.1`	DSE1_N	107	182	7e-10	39.2
LXL04_035273	`PF23414.2`	Beta-prop_EML_2	119	249	7.2e-17	62.3
LXL04_035273	`PF25173.2`	Beta-prop_WDR3_1st	130	306	5.5e-21	75.8
LXL04_035273	`PF24782.3`	WD40_MABP1-WDR62_2nd	142	265	1.6e-11	44.5
LXL04_035273	`PF23409.2`	Beta-prop_EML	147	307	2e-10	41.3
LXL04_035273	`PF25391.2`	WD40_Gbeta	150	308	2.2e-10	40.8
LXL04_035273	`PF23098.2`	Beta-prop_NOL10_N	164	305	7.5e-11	42.5
LXL04_035273	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	165	289	6.1e-07	29.7
LXL04_035273	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	166	301	5.4e-11	43.1
LXL04_035273	`PF24817.2`	WD40_WDHD1_1st	188	278	2.7e-12	47.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FFA7`	Arabidopsis thaliana	WD repeat-containing protein RUP2	60.486%	Swiss-Prot	strong database homology
`Q9LTJ6`	Arabidopsis thaliana	WD repeat-containing protein RUP1	57.522%	Swiss-Prot	strong database homology
`P43254`	Arabidopsis thaliana	E3 ubiquitin-protein ligase COP1	33.333%	Swiss-Prot	moderate database homology
`Q9LJR3`	Arabidopsis thaliana	Protein SPA1-RELATED 3	36.615%	Swiss-Prot	moderate database homology

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