LXL04_027963 | RubberDandelionOmics

Gene overview

LXL04_027963

Reference: OH-1004 Chr: Chr06 Coordinates: 27799838-27812843 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4233 bp · LXL04_027963|LXL04_027963|OH1004|cDNA

ATGTCCACCACCGCTGAGATCCTCCAACAAACCACCACCTTCCTCTCAGAAACACTCTCACAACCAGACATCCGCCGCCGTATATTCTCCATCCTCCGCAACAATTCCTCTCCTTCCGTCCAACTCAACATCAAACAGCTAAACCTCGCCGCTGACACACTTGAAAACGCCATAACCACCAGCAACTCCTCCGTCAAAACCTCCTCCCTCCGACTCTCCGAAAAGCTTCTCCTCTCACTCCCACAAAACCCGTTTTCCTC...

CDS

Download CDS FASTA

4233 bp · LXL04_027963|LXL04_027963|OH1004|CDS

ATGTCCACCACCGCTGAGATCCTCCAACAAACCACCACCTTCCTCTCAGAAACACTCTCACAACCAGACATCCGCCGCCGTATATTCTCCATCCTCCGCAACAATTCCTCTCCTTCCGTCCAACTCAACATCAAACAGCTAAACCTCGCCGCTGACACACTTGAAAACGCCATAACCACCAGCAACTCCTCCGTCAAAACCTCCTCCCTCCGACTCTCCGAAAAGCTTCTCCTCTCACTCCCACAAAACCCGTTTTCCTC...

Protein

Download Protein FASTA

1410 aa · LXL04_027963|LXL04_027963|OH1004|PROTEIN

MSTTAEILQQTTTFLSETLSQPDIRRRIFSILRNNSSPSVQLNIKQLNLAADTLENAITTSNSSVKTSSLRLSEKLLLSLPQNPFSSFLLSLIYTLCQRPIDASLTLLNLFQTDPSIARSEIAPQVFEDLFLINFLPVLEWYNEQRSRILSSLSSNAGYESDDNSVVMDSVVSCTTLLSKMNGNQASELKELERDYEQVLDENCRVFVGYFEEILGYKDGNRVIVPPSVVLEALHKGDQHVYNQDEKSISTQFGSKNGRY...

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_027963`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_027963

Location Chr06:27799838-27812843 (+)

Description Similar to CERBERUS: Putative E3 ubiquitin-protein ligase LIN-1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g71020`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g23030`	Functions as an E3 ubiquitin ligase.	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_027963 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009877 nodulation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

mtr:11418360

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.

Nucleus0.523

Rank 1 · LXL04_027963 · OH-1004

Cytoplasm0.396

Rank 2 · LXL04_027963 · OH-1004

Cell membrane0.115

Rank 3 · LXL04_027963 · OH-1004

Endoplasmic reticulum0.062

Rank 4 · LXL04_027963 · OH-1004

Lysosome / Vacuole0.045

Rank 5 · LXL04_027963 · 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.

PF23568.2ARM_LIN13-220 aa

PF04564.22U-box372-440 aa

PF23654.2ARM_LIN_2nd472-630 aa

PF23628.3ARM_LIN_C637-998 aa

PF24807.2WD40_CDC20-Fz1009-1096 aa

PF25173.2Beta-prop_WDR3_1st1022-1126 aa

PF24817.2WD40_WDHD1_1st1022-1115 aa

PF25175.2Beta-prop_WDR51024-1097 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027963	`PF23568.2`	ARM_LIN	13	220	8.2e-19	68.5
LXL04_027963	`PF04564.22`	U-box	372	440	8.6e-15	55.4
LXL04_027963	`PF23654.2`	ARM_LIN_2nd	472	630	3.7e-62	209.5
LXL04_027963	`PF23628.3`	ARM_LIN_C	637	998	8.4e-145	483.1
LXL04_027963	`PF24807.2`	WD40_CDC20-Fz	1009	1096	6.7e-12	46.0
LXL04_027963	`PF25173.2`	Beta-prop_WDR3_1st	1022	1126	4.6e-13	50.0
LXL04_027963	`PF24817.2`	WD40_WDHD1_1st	1022	1115	1.1e-12	48.5
LXL04_027963	`PF25175.2`	Beta-prop_WDR5	1024	1097	3.1e-09	37.2
LXL04_027963	`PF25172.2`	Beta-prop_WDR3_2nd	1025	1096	1.1e-11	45.2
LXL04_027963	`PF23409.2`	Beta-prop_EML	1026	1113	6.3e-09	36.4
LXL04_027963	`PF24814.2`	WD40_Prp19	1027	1115	5.9e-11	42.7
LXL04_027963	`PF24796.2`	WDR55	1028	1115	3.6e-08	33.5
LXL04_027963	`PF25174.2`	Beta-prop_THOC3	1032	1107	1.6e-12	47.7
LXL04_027963	`PF23381.2`	Beta-prop_IFT122_1st	1032	1144	7.5e-12	45.9
LXL04_027963	`PF00400.39`	WD40	1056	1091	2.1e-13	50.9
LXL04_027963	`PF24817.2`	WD40_WDHD1_1st	1321	1408	1.1e-12	48.5

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
`Q9C9A6`	Arabidopsis thaliana	U-box domain-containing protein 10	46.667%	Swiss-Prot	weak database homology
`Q8GUG9`	Arabidopsis thaliana	U-box domain-containing protein 11	52.174%	Swiss-Prot	weak database homology

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