LXL04_010623 | RubberDandelionOmics

Gene overview

LXL04_010623

Reference: OH-1004 Chr: Chr02 Coordinates: 149802334-149819718 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1170 bp · LXL04_010623|LXL04_010623|OH1004|cDNA

atgtcaggaggaattccgtacgtgatttcattgaaagctgtttcatctgcttcttctttttcaagatcttctgcggtaggaggaaaagttcctagttcagcaccaagggcctgttccgcaggggtagctattctagcagcagtagtacgaacatgtgTAGGCACCTTTGGGTTGCCTCCTAATATAATGTTTGTGCCTCTTCCAGCCATATTTGTGGATATGGTGATGGCGTATTTTCGTCCAGCTTGGGCAACAaaaaa...

CDS

Download CDS FASTA

1170 bp · LXL04_010623|LXL04_010623|OH1004|CDS

ATGTCAGGAGGAATTCCGTACGTGATTTCATTGAAAGCTGTTTCATCTGCTTCTTCTTTTTCAAGATCTTCTGCGGTAGGAGGAAAAGTTCCTAGTTCAGCACCAAGGGCCTGTTCCGCAGGGGTAGCTATTCTAGCAGCAGTAGTACGAACATGTGTAGGCACCTTTGGGTTGCCTCCTAATATAATGTTTGTGCCTCTTCCAGCCATATTTGTGGATATGGTGATGGCGTATTTTCGTCCAGCTTGGGCAACAAAAAA...

Protein

Download Protein FASTA

389 aa · LXL04_010623|LXL04_010623|OH1004|PROTEIN

MSGGIPYVISLKAVSSASSFSRSSAVGGKVPSSAPRACSAGVAILAAVVRTCVGTFGLPPNIMFVPLPAIFVDMVMAYFRPAWATKKEGYNGHGTESHTAKAWMVPVIPESFGYSLNIDWYNDDMAWHAIWLNGLSTTYLNKTNRQTYEAMNMTHPLSITLSKVKIDATRGDEVRLLEMNRDHRSRRSVRRRRRRWMKLLGFADREEEAMRTDEVQLLLDLRRQYQVAMNDGLIELIISKLSSTVVLILTNKSNIFVTVV...

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_010623`
TK1151 ID	TkA03G537700
OH-1004 ID	LXL04_010623
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.400
Protein coverage (%)	TK1151 83.415 / OH-1004 43.959 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_010623

Location Chr02:149802334-149819718 (+)

Description Similar to ATL46: RING-H2 finger protein ATL46

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g40250`	RING-H2 finger protein ATL46.	No verified direct reference in this release
`At1g53820`	RING-H2 finger protein ATL60.	No verified direct reference in this release
`At3g16720`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At4g40070`	RING-H2 finger protein ATL32.	No verified direct reference in this release
`At1g23980`	RING-H2 finger protein ATL47.	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_010623 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G23980

ath:AT1G53820

ath:AT3G16720

ath:AT4G40070

ath:AT5G40250

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 membrane0.314

Rank 1 · LXL04_010623 · OH-1004

Nucleus0.282

Rank 2 · LXL04_010623 · OH-1004

Cytoplasm0.216

Rank 3 · LXL04_010623 · OH-1004

Endoplasmic reticulum0.157

Rank 4 · LXL04_010623 · OH-1004

Mitochondrion0.110

Rank 5 · LXL04_010623 · 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_2298-340 aa

PF17123.12zf-RING_11298-326 aa

PF12678.14zf-rbx1315-340 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010623	`PF13639.13`	zf-RING_2	298	340	8.2e-12	45.9
LXL04_010623	`PF17123.12`	zf-RING_11	298	326	6.9e-07	29.6
LXL04_010623	`PF12678.14`	zf-rbx1	315	340	2.7e-07	31.4

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
`Q9FL07`	Arabidopsis thaliana	RING-H2 finger protein ATL46	31.783%	Swiss-Prot	weak database homology
`P0C035`	Arabidopsis thaliana	RING-H2 finger protein ATL60	60.417%	Swiss-Prot	weak database homology
`Q8L9T5`	Arabidopsis thaliana	RING-H2 finger protein ATL2	37.000%	Swiss-Prot	weak database homology
`Q8W571`	Arabidopsis thaliana	RING-H2 finger protein ATL32	41.791%	Swiss-Prot	weak database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	38.000%	Swiss-Prot	weak database homology

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