LXL04_025711 | RubberDandelionOmics

Gene overview

LXL04_025711

Reference: OH-1004 Chr: Chr05 Coordinates: 115671815-115672741 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

672 bp · LXL04_025711|LXL04_025711|OH1004|cDNA

ATGAATTCGATTTGCTGCTGTCAGTGTGGCGATGACCTTGAAGAATTCCCGACGAATGCTATATATAGACACTGCCTTTGCTTACGTTTCTTCTTCCACCAATTATTTACCGGATATGGTGCATTGTTTCAAAGAATCGAAGGATTACCAGTCTCATCTCCAATCCAAGGAACCTCATCGTCTTCCGTTGGCTTCACACTTCCAACCTCTTTAAACAATGAAAACCCTAACCACTCATCCACAAGACCTTTACCTTACGA...

CDS

Download CDS FASTA

672 bp · LXL04_025711|LXL04_025711|OH1004|CDS

ATGAATTCGATTTGCTGCTGTCAGTGTGGCGATGACCTTGAAGAATTCCCGACGAATGCTATATATAGACACTGCCTTTGCTTACGTTTCTTCTTCCACCAATTATTTACCGGATATGGTGCATTGTTTCAAAGAATCGAAGGATTACCAGTCTCATCTCCAATCCAAGGAACCTCATCGTCTTCCGTTGGCTTCACACTTCCAACCTCTTTAAACAATGAAAACCCTAACCACTCATCCACAAGACCTTTACCTTACGA...

Protein

Download Protein FASTA

223 aa · LXL04_025711|LXL04_025711|OH1004|PROTEIN

MNSICCCQCGDDLEEFPTNAIYRHCLCLRFFFHQLFTGYGALFQRIEGLPVSSPIQGTSSSSVGFTLPTSLNNENPNHSSTRPLPYESDHRFTRLQRGLVSRREKSITHFQEESQALRRSMSSSGMEFLDFGKRKSGIESPDDSKCGVPDSLEKVKVPEGVPYEQSSDNEDVCPTCLEEYTLENPKIVTQCSHHFHLGCIYEWMERSDTCPMCGKVMEFCESP

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_025711`
TK1151 ID	TkA08G340540
OH-1004 ID	LXL04_025711
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)	98.400
Protein coverage (%)	TK1151 98.930 / OH-1004 82.960 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_025711

Location Chr05:115671815-115672741 (+)

Description Similar to At3g02290: E3 ubiquitin-protein ligase At3g02290

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02290`	Mediates E2-dependent protein ubiquitination.	No verified direct reference in this release
`At4g23450`	Possesses E3 ubiquitin-protein ligase activity in vitro when associated with the E2 enzyme UBC8 in vitro.	The Arabidopsis C3H2C3-type RING E3 ubiquitin ligase AtAIRP1 is a positive regulator of an abscisic acid-dependent response to drought stress.2010 · DOI: 10.1104/pp.110.164749
`At4g00335`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At4g14220`	E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression.	Targeted degradation of the cyclin-dependent kinase inhibitor ICK4/KRP6 by RING-type E3 ligases is essential for mitotic cell cycle progression during Arabidopsis gametogenesis.2008 · DOI: 10.1105/tpc.108.059741

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025711 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009414 response to water deprivation Biological Process

GO:0009561 megagametogenesis Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010498 proteasomal protein catabolic process Biological Process

GO:0010729 positive regulation of hydrogen peroxide biosynthetic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036503 ERAD pathway Biological Process

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

GO:0051726 regulation of cell cycle Biological Process

GO:0055046 microgametogenesis Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT3G02290

ath:AT4G00335

ath:AT4G14220

ath:AT4G23450

xtr:779713

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.

Cytoplasm0.454

Rank 1 · LXL04_025711 · OH-1004

Nucleus0.439

Rank 2 · LXL04_025711 · OH-1004

Cell membrane0.122

Rank 3 · LXL04_025711 · OH-1004

Endoplasmic reticulum0.082

Rank 4 · LXL04_025711 · OH-1004

Mitochondrion0.079

Rank 5 · LXL04_025711 · 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-rbx1170-213 aa

PF12861.14zf-ANAPC11171-219 aa

PF13639.13zf-RING_2172-213 aa

PF13923.13zf-C3HC4_2173-213 aa

PF13445.13zf-RING_UBOX173-211 aa

PF00097.32zf-C3HC4173-213 aa

PF14634.13zf-RING_5173-215 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025711	`PF12678.14`	zf-rbx1	170	213	3.5e-11	43.9
LXL04_025711	`PF12861.14`	zf-ANAPC11	171	219	1.2e-06	29.2
LXL04_025711	`PF13639.13`	zf-RING_2	172	213	1.8e-11	44.8
LXL04_025711	`PF13923.13`	zf-C3HC4_2	173	213	2.2e-08	34.5
LXL04_025711	`PF13445.13`	zf-RING_UBOX	173	211	1.4e-06	28.9
LXL04_025711	`PF00097.32`	zf-C3HC4	173	213	1.6e-06	28.6
LXL04_025711	`PF14634.13`	zf-RING_5	173	215	4.4e-06	27.3

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
`Q8LE94`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At3g02290	39.831%	Swiss-Prot	moderate database homology
`Q93ZF6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase AIRP1	57.692%	Swiss-Prot	weak database homology
`Q2HIJ8`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHB1A	53.846%	Swiss-Prot	weak database homology
`Q4TU14`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHF1A	42.857%	Swiss-Prot	weak database homology

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