LXL04_028932 | RubberDandelionOmics

Gene overview

LXL04_028932

Reference: OH-1004 Chr: Chr06 Coordinates: 74974860-74976423 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1245 bp · LXL04_028932|LXL04_028932|OH1004|cDNA

ATGGATGTAGATCATAGTAAACAAGCTGTTGGTGGGATTGCTGCCCCAAAAAAGAGATCAGTCACTGGTGGCTCTCAAAATGGAACTCCTCAATTCTGCAACCGAATCGGTTGCTGTGGAAGACTTAACCACACTAAATTTACTAAAAACAAATGCATAGACAAACCTAAAGCTACAAAGCCTTCTGGAAGTTCATCAAAGACTTGTTCTTCAATTAATAATGTGAAAAAATCTCTTCCAAATTTAGAGAAAAAGATTTC...

CDS

Download CDS FASTA

1245 bp · LXL04_028932|LXL04_028932|OH1004|CDS

ATGGATGTAGATCATAGTAAACAAGCTGTTGGTGGGATTGCTGCCCCAAAAAAGAGATCAGTCACTGGTGGCTCTCAAAATGGAACTCCTCAATTCTGCAACCGAATCGGTTGCTGTGGAAGACTTAACCACACTAAATTTACTAAAAACAAATGCATAGACAAACCTAAAGCTACAAAGCCTTCTGGAAGTTCATCAAAGACTTGTTCTTCAATTAATAATGTGAAAAAATCTCTTCCAAATTTAGAGAAAAAGATTTC...

Protein

Download Protein FASTA

414 aa · LXL04_028932|LXL04_028932|OH1004|PROTEIN

MDVDHSKQAVGGIAAPKKRSVTGGSQNGTPQFCNRIGCCGRLNHTKFTKNKCIDKPKATKPSGSSSKTCSSINNVKKSLPNLEKKISSKTERIPKESSVLPNESGPQQRKLKSRNAEVPSSSSRIKKTSASSSVMENKSQTESNNGRRRRFFQGESSSSGKGKRVIVMSANEGGPTVSTSRISVSDPKNSRNWTCGRANGVSSIRTRRSLKMDSPKGSIDLSSFQSDDVITDTSQADTLSSSEETSVTSTDHQVVRFVNH...

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_028932`
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_028932

Location Chr06:74974860-74976423 (+)

Description Similar to HIP1: Probable E3 ubiquitin-protein ligase HIP1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`At5g42940`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`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
`Os01g0667700`	Probable E3 ubiquitin-protein ligase.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028932 · 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.

Nucleus0.664

Rank 1 · LXL04_028932 · OH-1004

Cytoplasm0.359

Rank 2 · LXL04_028932 · OH-1004

Cell membrane0.081

Rank 3 · LXL04_028932 · OH-1004

Endoplasmic reticulum0.040

Rank 4 · LXL04_028932 · OH-1004

Mitochondrion0.028

Rank 5 · LXL04_028932 · 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.

PF13639.13zf-RING_2363-405 aa

PF13923.13zf-C3HC4_2363-404 aa

PF17123.12zf-RING_11364-391 aa

PF00097.32zf-C3HC4364-404 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028932	`PF13639.13`	zf-RING_2	363	405	2.2e-12	47.8
LXL04_028932	`PF13923.13`	zf-C3HC4_2	363	404	4.6e-08	33.4
LXL04_028932	`PF17123.12`	zf-RING_11	364	391	4.6e-07	30.1
LXL04_028932	`PF00097.32`	zf-C3HC4	364	404	2.1e-06	28.2

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
`O49500`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR2	45.324%	Swiss-Prot	weak database homology
`Q9ZQF9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR1	42.500%	Swiss-Prot	weak database homology
`Q9FMM4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHG1A	41.892%	Swiss-Prot	weak database homology
`Q7XTV7`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase HIP1	47.857%	Swiss-Prot	weak database homology
`Q5QLR5`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase ZFP1	48.673%	Swiss-Prot	weak database homology

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