LXL04_006993 | RubberDandelionOmics

Gene overview

LXL04_006993

Reference: OH-1004 Chr: Chr02 Coordinates: 33036737-33039209 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1284 bp · LXL04_006993|LXL04_006993|OH1004|cDNA

AACTTTTGCTTAACGCCACGGCACCACTTCTCACGTTTCCTCCCCACCTTACATTCTCTCTCCCTCCAATTTAAACACAATAAACCCCCACACTTCACTCGCATTCTCTCTCGTCGTCGGTGGTATTTCCACATGGATTCCCAcctcaccaccaccaccacctcctccgTCTTCTCCGCCGTCTCCCCCGCAGATCATACTCCGACATCCGCTTCCATCACTCACACCCTCAGTCTCATCCAAGACAACAACCATGATCC...

CDS

Download CDS FASTA

1152 bp · LXL04_006993|LXL04_006993|OH1004|CDS

ATGGATTCCCACCTCACCACCACCACCACCTCCTCCGTCTTCTCCGCCGTCTCCCCCGCAGATCATACTCCGACATCCGCTTCCATCACTCACACCCTCAGTCTCATCCAAGACAACAACCATGATCCTTTTACGAAAATTCAAGCTGCGAAAGAGATCCGTCGGCTCACGAAAACATCACAGCGCTGCCGTCGTCAGTTTTCCGATGCAATCCTACCTCTTGTCTCCATGCTCCAGTCTCCTTCCGTGGAAGCTAAGGC...

Protein

Download Protein FASTA

383 aa · LXL04_006993|LXL04_006993|OH1004|PROTEIN

MDSHLTTTTTSSVFSAVSPADHTPTSASITHTLSLIQDNNHDPFTKIQAAKEIRRLTKTSQRCRRQFSDAILPLVSMLQSPSVEAKAAALLALLNLAVQDETNKIAIVDSGALEPIVTFLRSQNTNLQEYATASLATLSASVAKRSTIGKSGAIPFLVKIIDNGTPQAKMDAVLALSNLSSEFDNLKTILDSDPIPNLVTILKTSKKSSKISEKTTALLESLVSFEDGRVALTSEDGGVLAVVEVLERGSPQNREHAVGT...

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_006993`
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_006993

Location Chr02:33036737-33039209 (+)

Description Similar to PUB4: U-box domain-containing protein 4

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g23140`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g54790`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g67340`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g46510`	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_006993 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0090333 regulation of stomatal closure Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G23030

ath:AT2G23140

ath:AT3G46510

ath:AT3G54790

ath:AT5G67340

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.

Cytoplasm0.580

Rank 1 · LXL04_006993 · OH-1004

Nucleus0.419

Rank 2 · LXL04_006993 · OH-1004

Cell membrane0.117

Rank 3 · LXL04_006993 · OH-1004

Endoplasmic reticulum0.048

Rank 4 · LXL04_006993 · OH-1004

Lysosome / Vacuole0.035

Rank 5 · LXL04_006993 · 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.

PF24768.2ARM_ARMC528-225 aa

PF25598.2ARM_PUB45-309 aa

PF03224.21V-ATPase_H_N66-247 aa

PF00514.30Arm103-140 aa

PF00514.30Arm144-181 aa

PF24768.2ARM_ARMC5175-308 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006993	`PF24768.2`	ARM_ARMC5	28	225	2e-19	70.8
LXL04_006993	`PF25598.2`	ARM_PUB	45	309	4.1e-16	60.0
LXL04_006993	`PF03224.21`	V-ATPase_H_N	66	247	1.3e-07	32.1
LXL04_006993	`PF00514.30`	Arm	103	140	1e-18	67.3
LXL04_006993	`PF00514.30`	Arm	144	181	1e-18	67.3
LXL04_006993	`PF24768.2`	ARM_ARMC5	175	308	2e-19	70.8

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
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	36.466%	Swiss-Prot	moderate database homology
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	37.102%	Swiss-Prot	moderate database homology
`Q5XEZ8`	Arabidopsis thaliana	U-box domain-containing protein 2	34.812%	Swiss-Prot	moderate database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	35.094%	Swiss-Prot	moderate database homology
`Q8GUG9`	Arabidopsis thaliana	U-box domain-containing protein 11	33.962%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card