LXL04_027023 | RubberDandelionOmics

Gene overview

LXL04_027023

Reference: OH-1004 Chr: Chr06 Coordinates: 7130519-7134369 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2076 bp · LXL04_027023|LXL04_027023|OH1004|cDNA

ATGGGAGGTGGAGGCGGCTCAATCGGAGGACCGATTGTACCGTCGGTGAAGTCTGGTCTGCCTGAGCCGTCAACGGAAATACCAGCTCCTGCTTCAATTCCGCCACATCCGTCGCATGCTCCGCCTTCGGATTTCGCGGCGGTAGAGGTGAAGCTCAAGGAGGAGGATCAAGAGTTGGCGGAGACGGATAAGGATATGTTATGTCCGATATGCATGCAGATAATCAAGGACGCCTTTTTGACATCATGTGGTCATAGTTT...

CDS

Download CDS FASTA

2076 bp · LXL04_027023|LXL04_027023|OH1004|CDS

ATGGGAGGTGGAGGCGGCTCAATCGGAGGACCGATTGTACCGTCGGTGAAGTCTGGTCTGCCTGAGCCGTCAACGGAAATACCAGCTCCTGCTTCAATTCCGCCACATCCGTCGCATGCTCCGCCTTCGGATTTCGCGGCGGTAGAGGTGAAGCTCAAGGAGGAGGATCAAGAGTTGGCGGAGACGGATAAGGATATGTTATGTCCGATATGCATGCAGATAATCAAGGACGCCTTTTTGACATCATGTGGTCATAGTTT...

Protein

Download Protein FASTA

691 aa · LXL04_027023|LXL04_027023|OH1004|PROTEIN

MGGGGGSIGGPIVPSVKSGLPEPSTEIPAPASIPPHPSHAPPSDFAAVEVKLKEEDQELAETDKDMLCPICMQIIKDAFLTSCGHSFCYLCIVTHLQNKNDCPSCASYLTTNQIFPNFLLNKLLMKASARHIAQHSSPTEHLRQALQQGCDVSVKEVDILLVLLSEKKRKMEQEEAETNLQIMREFLHSLRKQKLEELNEIQNDLQYIKEDINAVERQRLELHRAREKYSVKLRMLSDDPHNVRSSWPSLMDKRNSSNMS...

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_027023`
TK1151 ID	TkA07G025820
OH-1004 ID	LXL04_027023
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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	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_027023

Location Chr06:7130519-7134369 (-)

Description Similar to COP1: E3 ubiquitin-protein ligase COP1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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_027023 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process 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:0009963 positive regulation of flavonoid biosynthetic process Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0010212 response to ionizing radiation Biological Process

GO:0010224 response to UV-B Biological Process

GO:0016567 protein ubiquitination Biological Process

KEGG gene cross-reference

ath:AT2G32950

ath:AT3G15354

hsa:64326

mmu:26374

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.

Nucleus0.593

Rank 1 · LXL04_027023 · OH-1004

Cytoplasm0.380

Rank 2 · LXL04_027023 · OH-1004

Lysosome / Vacuole0.052

Rank 3 · LXL04_027023 · OH-1004

Cell membrane0.048

Rank 4 · LXL04_027023 · OH-1004

Golgi apparatus0.043

Rank 5 · LXL04_027023 · 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.

PF13920.13zf-C3HC4_365-108 aa

PF13639.13zf-RING_267-105 aa

PF13923.13zf-C3HC4_268-105 aa

PF00097.32zf-C3HC468-105 aa

PF13445.13zf-RING_UBOX68-103 aa

PF23389.2Beta-prop_WDR19_1st379-507 aa

PF24796.2WDR55385-628 aa

PF25173.2Beta-prop_WDR3_1st386-512 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027023	`PF13920.13`	zf-C3HC4_3	65	108	8.5e-07	29.4
LXL04_027023	`PF13639.13`	zf-RING_2	67	105	2.9e-06	28.1
LXL04_027023	`PF13923.13`	zf-C3HC4_2	68	105	2.7e-11	43.8
LXL04_027023	`PF00097.32`	zf-C3HC4	68	105	6.8e-10	39.4
LXL04_027023	`PF13445.13`	zf-RING_UBOX	68	103	2.7e-06	28.0
LXL04_027023	`PF23389.2`	Beta-prop_WDR19_1st	379	507	6e-10	39.4
LXL04_027023	`PF24796.2`	WDR55	385	628	6.4e-17	62.2
LXL04_027023	`PF25173.2`	Beta-prop_WDR3_1st	386	512	8.2e-29	101.3
LXL04_027023	`PF25175.2`	Beta-prop_WDR5	387	634	9.1e-34	117.8
LXL04_027023	`PF23775.2`	Beta-prop_RIG_2nd	388	499	7.4e-14	52.5
LXL04_027023	`PF25172.2`	Beta-prop_WDR3_2nd	392	511	4.9e-14	53.0
LXL04_027023	`PF24805.2`	EIF3I	392	509	2.1e-11	44.3
LXL04_027023	`PF29037.1`	DSE1_N	398	512	2.7e-10	40.6
LXL04_027023	`PF24780.2`	WD40_MABP1-WDR62_1st	424	551	1.3e-09	38.5
LXL04_027023	`PF23609.2`	Beta-prop_EIPR1	435	507	1.9e-12	47.9
LXL04_027023	`PF25174.2`	Beta-prop_THOC3	436	554	3.8e-33	115.4

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
`P43254`	Arabidopsis thaliana	E3 ubiquitin-protein ligase COP1	67.784%	Swiss-Prot	strong database homology
`Q9LJR3`	Arabidopsis thaliana	Protein SPA1-RELATED 3	36.620%	Swiss-Prot	moderate database homology

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