LXL04_003204 | RubberDandelionOmics

Gene overview

LXL04_003204

Reference: OH-1004 Chr: Chr01 Coordinates: 70843485-70845806 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

879 bp · LXL04_003204|LXL04_003204|OH1004|cDNA

ATGGATTCATTGTTAGCACATTCATCAATGGCAGgtgaaccgatcatgcctcaGGTTGGTGTTACTGCTGATGATCGCACTTCAGAGGAGGATGTCTGCAGTATATGCCTCGACGATTTTGACTCTTATGAAAACCCTTCCGCTGTAACAACCTGCAAGCATGCATTTCATCTCCAGTGTATTATTGAGTGGTCACAGAGAAGCAAAGAATGCCCAATATGTTGGCAGTTGATTCTGTTGAAGGATCCAGCCAGTCAAGA...

CDS

Download CDS FASTA

879 bp · LXL04_003204|LXL04_003204|OH1004|CDS

ATGGATTCATTGTTAGCACATTCATCAATGGCAGGTGAACCGATCATGCCTCAGGTTGGTGTTACTGCTGATGATCGCACTTCAGAGGAGGATGTCTGCAGTATATGCCTCGACGATTTTGACTCTTATGAAAACCCTTCCGCTGTAACAACCTGCAAGCATGCATTTCATCTCCAGTGTATTATTGAGTGGTCACAGAGAAGCAAAGAATGCCCAATATGTTGGCAGTTGATTCTGTTGAAGGATCCAGCCAGTCAAGA...

Protein

Download Protein FASTA

292 aa · LXL04_003204|LXL04_003204|OH1004|PROTEIN

MDSLLAHSSMAGEPIMPQVGVTADDRTSEEDVCSICLDDFDSYENPSAVTTCKHAFHLQCIIEWSQRSKECPICWQLILLKDPASQELLSMVEDERSARSVITVRHTYEDPEVDHDIEYNDTHFEEEVMGSFGGRRQKQRVSGVGPSVRTIGQEMYTSLEEFHTSSMEDCTSVVDNQTPNGSPGRPIAVDMHAFSESVKSKFTAASARYKESITKGTQGLKEKLLAKNSPVKELSRGVQREMSRIFERLDPTSKRPSPSS...

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_003204`
TK1151 ID	TkA01G385820
OH-1004 ID	LXL04_003204
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

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_003204

Location Chr01:70843485-70845806 (+)

Description Similar to RHF1A: E3 ubiquitin-protein ligase RHF1A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At5g22000`	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
`At4g00335`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003204 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009561 megagametogenesis Biological Process

GO:0010498 proteasomal protein catabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051603 proteolysis involved in protein catabolic process Biological Process

GO:0051726 regulation of cell cycle Biological Process

GO:0055046 microgametogenesis Biological Process

GO:0005634 nucleus 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:AT4G00335

ath:AT4G14220

ath:AT5G22000

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.

Cytoplasm0.578

Rank 1 · LXL04_003204 · OH-1004

Nucleus0.352

Rank 2 · LXL04_003204 · OH-1004

Cell membrane0.120

Rank 3 · LXL04_003204 · OH-1004

Golgi apparatus0.080

Rank 4 · LXL04_003204 · OH-1004

Mitochondrion0.076

Rank 5 · LXL04_003204 · 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.

PF12678.14zf-rbx127-74 aa

PF13639.13zf-RING_232-74 aa

PF13923.13zf-C3HC4_233-74 aa

PF13445.13zf-RING_UBOX33-72 aa

PF17123.12zf-RING_1133-61 aa

PF00097.32zf-C3HC433-74 aa

PF14634.13zf-RING_533-74 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003204	`PF12678.14`	zf-rbx1	27	74	7.6e-09	36.4
LXL04_003204	`PF13639.13`	zf-RING_2	32	74	1.3e-11	45.3
LXL04_003204	`PF13923.13`	zf-C3HC4_2	33	74	3.9e-10	40.1
LXL04_003204	`PF13445.13`	zf-RING_UBOX	33	72	4.9e-09	36.8
LXL04_003204	`PF17123.12`	zf-RING_11	33	61	6e-08	33.0
LXL04_003204	`PF00097.32`	zf-C3HC4	33	74	1e-07	32.4
LXL04_003204	`PF14634.13`	zf-RING_5	33	74	3.8e-06	27.5

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
`Q4TU14`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHF1A	58.065%	Swiss-Prot	weak database homology
`Q9ZT42`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHF2A	47.664%	Swiss-Prot	weak database homology
`Q2HIJ8`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHB1A	50.000%	Swiss-Prot	weak database homology
`Q8LE94`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At3g02290	50.000%	Swiss-Prot	weak database homology
`Q93ZF6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase AIRP1	47.727%	Swiss-Prot	weak database homology

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