LXL04_017990 | RubberDandelionOmics

Gene overview

LXL04_017990

Reference: OH-1004 Chr: Chr04 Coordinates: 4704087-4705316 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1230 bp · LXL04_017990|LXL04_017990|OH1004|cDNA

ATGGGCTACAAATCCCCATGGCATCCAACTCCATTGATGCTCTTCCTTGTATCCACAACCCCCTCCGTAACCACCTCGTCGTTTGCCAGTCCTCCGCCACCGCTAACGCCTCCGCCGagatcaccaccaccaccaaacTCAACGGTCAAGCCAAGCATGACGATCATTATCGGTCTTCTCACCACCATATTCTCCATCACTTTTCTTATACTCCTATACGCCAAACACTGCCGTCGGTCGCATAATGCGTACCAGCCGGG...

CDS

Download CDS FASTA

1230 bp · LXL04_017990|LXL04_017990|OH1004|CDS

ATGGGCTACAAATCCCCATGGCATCCAACTCCATTGATGCTCTTCCTTGTATCCACAACCCCCTCCGTAACCACCTCGTCGTTTGCCAGTCCTCCGCCACCGCTAACGCCTCCGCCGAGATCACCACCACCACCAAACTCAACGGTCAAGCCAAGCATGACGATCATTATCGGTCTTCTCACCACCATATTCTCCATCACTTTTCTTATACTCCTATACGCCAAACACTGCCGTCGGTCGCATAATGCGTACCAGCCGGG...

Protein

Download Protein FASTA

409 aa · LXL04_017990|LXL04_017990|OH1004|PROTEIN

MGYKSPWHPTPLMLFLVSTTPSVTTSSFASPPPPLTPPPRSPPPPNSTVKPSMTIIIGLLTTIFSITFLILLYAKHCRRSHNAYQPGGEIMAVRSTDRENSGIDRTIIESLPVFRFGSLSGQKDGLECAVCLSRFDPTEVLRLLPKCKHAFHVECVDTWLDAHSTCPLCRYRVDPEDIFLVLGENEYSRDIERLPEVKAEEEKESEIAVRRVSGRHSSAGEKGTGLQISVEPSSPLPAAVAGSRRSLDSSNAKKKTTRKT...

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_017990`
TK1151 ID	TkA08G034880
OH-1004 ID	LXL04_017990
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	93.500
Protein coverage (%)	TK1151 100.000 / OH-1004 97.066 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_017990

Location Chr04:4704087-4705316 (-)

Description Similar to ATL43: RING-H2 finger protein ATL43

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g05810`	RING-H2 finger protein ATL43.	No verified direct reference in this release
`At2g20030`	Putative RING-H2 finger protein ATL12.	No verified direct reference in this release
`At4g28890`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At4g40070`	RING-H2 finger protein ATL32.	No verified direct reference in this release
`At3g05200`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	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_017990 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane 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:AT2G20030

ath:AT3G05200

ath:AT4G28890

ath:AT4G40070

ath:AT5G05810

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.

Cell membrane0.545

Rank 1 · LXL04_017990 · OH-1004

Nucleus0.317

Rank 2 · LXL04_017990 · OH-1004

Cytoplasm0.210

Rank 3 · LXL04_017990 · OH-1004

Endoplasmic reticulum0.100

Rank 4 · LXL04_017990 · OH-1004

Golgi apparatus0.040

Rank 5 · LXL04_017990 · 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.

PF13639.13zf-RING_2127-170 aa

PF17123.12zf-RING_11127-156 aa

PF13923.13zf-C3HC4_2127-169 aa

PF00097.32zf-C3HC4128-169 aa

PF12678.14zf-rbx1140-170 aa

PF12861.14zf-ANAPC11143-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017990	`PF13639.13`	zf-RING_2	127	170	5.5e-14	52.9
LXL04_017990	`PF17123.12`	zf-RING_11	127	156	6e-10	39.4
LXL04_017990	`PF13923.13`	zf-C3HC4_2	127	169	7e-08	32.9
LXL04_017990	`PF00097.32`	zf-C3HC4	128	169	1.3e-06	28.9
LXL04_017990	`PF12678.14`	zf-rbx1	140	170	1.8e-08	35.2
LXL04_017990	`PF12861.14`	zf-ANAPC11	143	172	7.5e-06	26.6

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
`Q5EAE9`	Arabidopsis thaliana	RING-H2 finger protein ATL43	48.413%	Swiss-Prot	moderate database homology
`Q9SL78`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL12	34.530%	Swiss-Prot	moderate database homology
`Q5XF85`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL42	34.259%	Swiss-Prot	moderate database homology
`Q8W571`	Arabidopsis thaliana	RING-H2 finger protein ATL32	40.146%	Swiss-Prot	weak database homology
`Q8RXX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL6	32.317%	Swiss-Prot	weak database homology

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