LXL04_006165 | RubberDandelionOmics

Gene overview

LXL04_006165

Reference: OH-1004 Chr: Chr02 Coordinates: 2965887-2971340 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1452 bp · LXL04_006165|LXL04_006165|OH1004|cDNA

ATGGGAGCTAATCCCGAGCTCGTAGGTCTATTTCCTGAGAAGAAGCGCTCCAGAAACCCCTTCGTCCCTATTGGTGCATTGATAACAGCCGGGGTGCTGACAGCTGGCTTAATTAGTTTCAAGAAAGGGAACTCGCAGTTGGGTCAGAGTTTGATGCGGGCCCGTGTGGTTGCTCAGGGTGCAACCGTTGCACTCATGctCATTTTTCCCGAACAAGCCCAAAGACAAGTTAAAGGCCCGGTTGAACCTAATTTTTTAGC...

CDS

Download CDS FASTA

1452 bp · LXL04_006165|LXL04_006165|OH1004|CDS

ATGGGAGCTAATCCCGAGCTCGTAGGTCTATTTCCTGAGAAGAAGCGCTCCAGAAACCCCTTCGTCCCTATTGGTGCATTGATAACAGCCGGGGTGCTGACAGCTGGCTTAATTAGTTTCAAGAAAGGGAACTCGCAGTTGGGTCAGAGTTTGATGCGGGCCCGTGTGGTTGCTCAGGGTGCAACCGTTGCACTCATGCTCATTTTTCCCGAACAAGCCCAAAGACAAGTTAAAGGCCCGGTTGAACCTAATTTTTTAGC...

Protein

Download Protein FASTA

483 aa · LXL04_006165|LXL04_006165|OH1004|PROTEIN

MGANPELVGLFPEKKRSRNPFVPIGALITAGVLTAGLISFKKGNSQLGQSLMRARVVAQGATVALMLIFPEQAQRQVKGPVEPNFLAPPNTTELEGGVDLFKAFKVEISSMVSFRHTNVMKYQIYKEDGFVGFQQSTPYPPSPPSVQSYSPPFTVTFHRASASSSSSGPKISPAVLFIIVILAVLFFISGLLHLLVRFLTKHNSQSQSNRFPDGSPSETLQRQLQQLFHLHDSGLDQTFIDALPVFMYKEVVGAHEPFDC...

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_006165`
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_006165

Location Chr02:2965887-2971340 (-)

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
`At1g23980`	RING-H2 finger protein ATL47.	No verified direct reference in this release
`At2g18650`	May be involved in female gametophyte development.	No verified direct reference in this release
`At3g48030`	RING-H2 finger protein ATL48.	No verified direct reference in this release
`At4g30400`	RING-H2 finger protein ATL13.	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_006165 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus 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:AT2G18650

ath:AT3G48030

ath:AT5G40250

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.

Endoplasmic reticulum0.276

Rank 1 · LXL04_006165 · OH-1004

Cell membrane0.264

Rank 2 · LXL04_006165 · OH-1004

Nucleus0.230

Rank 3 · LXL04_006165 · OH-1004

Cytoplasm0.190

Rank 4 · LXL04_006165 · OH-1004

Golgi apparatus0.131

Rank 5 · LXL04_006165 · 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.

PF04588.19HIG_1_N19-68 aa

PF12861.14zf-ANAPC11257-305 aa

PF13639.13zf-RING_2259-302 aa

PF17123.12zf-RING_11259-288 aa

PF12678.14zf-rbx1259-302 aa

PF00097.32zf-C3HC4260-301 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006165	`PF04588.19`	HIG_1_N	19	68	1.4e-19	70.7
LXL04_006165	`PF12861.14`	zf-ANAPC11	257	305	7.3e-06	26.6
LXL04_006165	`PF13639.13`	zf-RING_2	259	302	6.4e-14	52.7
LXL04_006165	`PF17123.12`	zf-RING_11	259	288	1.7e-09	37.9
LXL04_006165	`PF12678.14`	zf-rbx1	259	302	4.6e-09	37.1
LXL04_006165	`PF00097.32`	zf-C3HC4	260	301	6.4e-06	26.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FL07`	Arabidopsis thaliana	RING-H2 finger protein ATL46	56.941%	Swiss-Prot	moderate database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	54.181%	Swiss-Prot	moderate database homology
`Q9ZV53`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL49	41.003%	Swiss-Prot	moderate database homology
`Q7X843`	Arabidopsis thaliana	RING-H2 finger protein ATL48	43.478%	Swiss-Prot	moderate database homology
`Q940Q4`	Arabidopsis thaliana	RING-H2 finger protein ATL13	40.066%	Swiss-Prot	weak database homology

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