LXL04_012377 | RubberDandelionOmics

Gene overview

LXL04_012377

Reference: OH-1004 Chr: Chr03 Coordinates: 11357754-11358971 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1218 bp · LXL04_012377|LXL04_012377|OH1004|cDNA

ATGTCAACGGTTGGGTCTTCATCATCGTCACACTGGTGCTACAGATGCAATCGATTTATTAGGGTTCGAATCAATCAAGAAGATTCATCTTTATCTTGTCCCGATTGCAACGGAGGTTTCATAGAGGAGATAGATAGCCCCAATAGATTAAATGGGTCGGTGATCTCGGACTTTCACCGAAGTCGGTCTCCTGCTGCGGCCATGTACATGGTCGGAAACGGCCAACAAAGCCCCGTGCCGAGCCCTAGCCCGCCGTTACT...

CDS

Download CDS FASTA

1218 bp · LXL04_012377|LXL04_012377|OH1004|CDS

ATGTCAACGGTTGGGTCTTCATCATCGTCACACTGGTGCTACAGATGCAATCGATTTATTAGGGTTCGAATCAATCAAGAAGATTCATCTTTATCTTGTCCCGATTGCAACGGAGGTTTCATAGAGGAGATAGATAGCCCCAATAGATTAAATGGGTCGGTGATCTCGGACTTTCACCGAAGTCGGTCTCCTGCTGCGGCCATGTACATGGTCGGAAACGGCCAACAAAGCCCCGTGCCGAGCCCTAGCCCGCCGTTACT...

Protein

Download Protein FASTA

405 aa · LXL04_012377|LXL04_012377|OH1004|PROTEIN

MSTVGSSSSSHWCYRCNRFIRVRINQEDSSLSCPDCNGGFIEEIDSPNRLNGSVISDFHRSRSPAAAMYMVGNGQQSPVPSPSPPLLRRARRNVGERSPFNPVIVLRGPTSTPEEPGSGTEESGTGGGFELYYDDGAGSGLRPLPASMSEFLLGSGFDRLLDQLAQIEGNGLGRIDNNPPASKAAIEAMPNIEIQENHVSIESYCAVCKEPFDLGSEAKEMPCQHLYHSDCILPWLALRNSCPVCRHELPTETTDSGDHQ...

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_012377`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_012377

Location Chr03:11357754-11358971 (-)

Description Similar to RHC2A: Probable E3 ubiquitin-protein ligase RHC2A

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g39720`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At3g46620`	E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid-dependent drought stress responses.	Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces tolerance to ABA-mediated drought stress.2012 · DOI: 10.1016/j.bbrc.2012.02.131 The E3 ligase AtRDUF1 positively regulates salt stress responses in Arabidopsis thaliana.2013 · DOI: 10.1371/journal.pone.0071078
`At5g59550`	E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid-dependent drought stress responses.	Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces tolerance to ABA-mediated drought stress.2012 · DOI: 10.1016/j.bbrc.2012.02.131
`At3g19950`	E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012377 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009414 response to water deprivation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0090378 seed trichome elongation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G39720

ath:AT3G19950

ath:AT3G46620

ath:AT5G59550

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.

Cytoplasm0.446

Rank 1 · LXL04_012377 · OH-1004

Nucleus0.364

Rank 2 · LXL04_012377 · OH-1004

Cell membrane0.222

Rank 3 · LXL04_012377 · OH-1004

Lysosome / Vacuole0.097

Rank 4 · LXL04_012377 · OH-1004

Endoplasmic reticulum0.094

Rank 5 · LXL04_012377 · OH-1004

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.

PF14369.12Zn_ribbon_199-44 aa

PF12678.14zf-rbx1200-246 aa

PF13923.13zf-C3HC4_2204-245 aa

PF13639.13zf-RING_2205-246 aa

PF00097.32zf-C3HC4205-245 aa

PF17123.12zf-RING_11205-232 aa

PF06547.18DUF1117275-387 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012377	`PF14369.12`	Zn_ribbon_19	9	44	1.6e-14	54.5
LXL04_012377	`PF12678.14`	zf-rbx1	200	246	7.4e-08	33.2
LXL04_012377	`PF13923.13`	zf-C3HC4_2	204	245	3.4e-08	33.9
LXL04_012377	`PF13639.13`	zf-RING_2	205	246	1e-11	45.6
LXL04_012377	`PF00097.32`	zf-C3HC4	205	245	5.5e-06	26.9
LXL04_012377	`PF17123.12`	zf-RING_11	205	232	6.2e-06	26.5
LXL04_012377	`PF06547.18`	DUF1117	275	387	2.1e-40	138.5

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
`O22283`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHC2A	51.198%	Swiss-Prot	strong database homology
`Q9SNB6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RDUF1	48.083%	Swiss-Prot	moderate database homology
`Q940T5`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RDUF2	49.541%	Swiss-Prot	moderate database homology
`Q8LPN7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1-like	31.660%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card