LXL04_038554 | RubberDandelionOmics

Gene overview

LXL04_038554

Reference: OH-1004 Chr: Chr09 Coordinates: 43874602-43875192 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

591 bp · LXL04_038554|LXL04_038554|OH1004|cDNA

ATGAATCCATACCTACGTAACACCTCTTTTCCAAACGCATACTTGACACAATATCCACAGTATTCCCACCACTCTAATTTCCCGTTCAATGGCTACCTGAACCTCGATACTCATACCCACCAACGTCCGGTGCCCGGAGGACGGAACTCTGCTAAATGGTCTGTAGATGAAGACGAAGTAGTTATTCTCGACAGTCTcgacatgtattcaccaccgccgccgccgcAGCCATCTTTCTCCATCCGTACACACCAACCGCT...

CDS

Download CDS FASTA

591 bp · LXL04_038554|LXL04_038554|OH1004|CDS

ATGAATCCATACCTACGTAACACCTCTTTTCCAAACGCATACTTGACACAATATCCACAGTATTCCCACCACTCTAATTTCCCGTTCAATGGCTACCTGAACCTCGATACTCATACCCACCAACGTCCGGTGCCCGGAGGACGGAACTCTGCTAAATGGTCTGTAGATGAAGACGAAGTAGTTATTCTCGACAGTCTCGACATGTATTCACCACCGCCGCCGCCGCAGCCATCTTTCTCCATCCGTACACACCAACCGCT...

Protein

Download Protein FASTA

196 aa · LXL04_038554|LXL04_038554|OH1004|PROTEIN

MNPYLRNTSFPNAYLTQYPQYSHHSNFPFNGYLNLDTHTHQRPVPGGRNSAKWSVDEDEVVILDSLDMYSPPPPPQPSFSIRTHQPLQFMGGRGHHQQSSEIIDEVVILENLNTNENSRLGGLTKEVISKNLKLKQINCSEEDDKDEICVICQVGFERKEMVGVLECKHCYHVECINEWLFHKNVCPLCKTRVFIV

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_038554`
TK1151 ID	TkA04G441770
OH-1004 ID	LXL04_038554
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_038554

Location Chr09:43874602-43875192 (+)

Description Similar to RHG1A: Probable E3 ubiquitin-protein ligase RHG1A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g42940`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At2g15530`	E3 ubiquitin-protein ligase that functions as a regulator of MED25 stability by targeting MED25 for degradation in a RING-H2- dependent way.	Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.2012 · DOI: 10.1104/pp.112.205500
`At4g34040`	E3 ubiquitin-protein ligase that functions as a regulator of MED25 stability by targeting MED25 for degradation in a RING-H2- dependent way.	Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.2012 · DOI: 10.1104/pp.112.205500

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0667700`	Probable E3 ubiquitin-protein ligase.	No verified direct reference in this release
`Os04g0648800`	Probable E3 ubiquitin-protein ligase that functions downstream of HAL3 and is required for HAL3-regulated plant growth.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_038554 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009845 seed germination Biological Process

GO:0009908 flower development Biological Process

GO:0010218 response to far red light Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0016567 protein ubiquitination Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

GO:0061659 ubiquitin-like protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G15530

ath:AT4G34040

ath:AT5G42940

dosa:Os01g0667700

dosa:Os04g0648800

osa:4326322

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.

Nucleus0.586

Rank 1 · LXL04_038554 · OH-1004

Cytoplasm0.515

Rank 2 · LXL04_038554 · OH-1004

Endoplasmic reticulum0.049

Rank 3 · LXL04_038554 · OH-1004

Cell membrane0.048

Rank 4 · LXL04_038554 · OH-1004

Lysosome / Vacuole0.043

Rank 5 · LXL04_038554 · 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.

PF12678.14zf-rbx1146-190 aa

PF13639.13zf-RING_2149-190 aa

PF17123.12zf-RING_11149-176 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038554	`PF12678.14`	zf-rbx1	146	190	4.5e-08	33.9
LXL04_038554	`PF13639.13`	zf-RING_2	149	190	2.9e-11	44.1
LXL04_038554	`PF17123.12`	zf-RING_11	149	176	3.3e-06	27.4

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
`Q9FMM4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHG1A	34.783%	Swiss-Prot	moderate database homology
`Q9ZQF9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR1	32.231%	Swiss-Prot	moderate database homology
`O49500`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR2	38.889%	Swiss-Prot	weak database homology
`Q5QLR5`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase ZFP1	34.615%	Swiss-Prot	weak database homology
`Q7XTV7`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase HIP1	33.043%	Swiss-Prot	moderate database homology

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