LXL04_028283 | RubberDandelionOmics

Gene overview

LXL04_028283

Reference: OH-1004 Chr: Chr06 Coordinates: 36709552-36710949 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1398 bp · LXL04_028283|LXL04_028283|OH1004|cDNA

ATGGATCGGAAAATCTTAGATTCCAATTACGAAAGACCTTACTATTATAATCGGCCACCTTTatcaccaccgccaccgccaccaccacctccaGCCACCGCCAATCACCTATCCCATGGTTTCAATCTAAACGATAAGGTGAGCCCAAGTGTTCTACTCATCATCATAATTCTCGCAATGATTTTCTTCATTTCTGGGTTGCTCCATCTTCTTGTTAGATTCTTTATGAGGCCAACTAATAGGGATCCCGACGAGTTCGA...

CDS

Download CDS FASTA

1398 bp · LXL04_028283|LXL04_028283|OH1004|CDS

ATGGATCGGAAAATCTTAGATTCCAATTACGAAAGACCTTACTATTATAATCGGCCACCTTTATCACCACCGCCACCGCCACCACCACCTCCAGCCACCGCCAATCACCTATCCCATGGTTTCAATCTAAACGATAAGGTGAGCCCAAGTGTTCTACTCATCATCATAATTCTCGCAATGATTTTCTTCATTTCTGGGTTGCTCCATCTTCTTGTTAGATTCTTTATGAGGCCAACTAATAGGGATCCCGACGAGTTCGA...

Protein

Download Protein FASTA

465 aa · LXL04_028283|LXL04_028283|OH1004|PROTEIN

MDRKILDSNYERPYYYNRPPLSPPPPPPPPPATANHLSHGFNLNDKVSPSVLLIIIILAMIFFISGLLHLLVRFFMRPTNRDPDEFDNVTALQGQLQQLFHLHDSGVDQSFIDTLPVFTYKSIIGVKDPFDCAVCLCEFEGADKLRLLPKCSHAFHMDCIDTWLLSHSTCPLCRGSLLADFTPNSCCSPFVLVLESGSSEISREIVNSDHHQANTSSIQRVNSHLSNGEFEFDKCEMVKEEENKEKVVTIKLGKFKNVDG...

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_028283`
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_028283

Location Chr06:36709552-36710949 (+)

Description Similar to ATL49: Putative RING-H2 finger protein ATL49

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g18650`	May be involved in female gametophyte development.	No verified direct reference in this release
`At4g30400`	RING-H2 finger protein ATL13.	No verified direct reference in this release
`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
`At5g57750`	Putative RING-H2 finger protein ATL50.	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_028283 · 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: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:AT2G18650

ath:AT4G30400

ath:AT5G40250

ath:AT5G57750

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 membrane0.420

Rank 1 · LXL04_028283 · OH-1004

Nucleus0.317

Rank 2 · LXL04_028283 · OH-1004

Cytoplasm0.257

Rank 3 · LXL04_028283 · OH-1004

Endoplasmic reticulum0.121

Rank 4 · LXL04_028283 · OH-1004

Lysosome / Vacuole0.061

Rank 5 · LXL04_028283 · 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.

PF12678.14zf-rbx1129-174 aa

PF12861.14zf-ANAPC11129-176 aa

PF13639.13zf-RING_2131-174 aa

PF17123.12zf-RING_11131-160 aa

PF13923.13zf-C3HC4_2132-173 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028283	`PF12678.14`	zf-rbx1	129	174	2.1e-10	41.4
LXL04_028283	`PF12861.14`	zf-ANAPC11	129	176	3.1e-07	31.1
LXL04_028283	`PF13639.13`	zf-RING_2	131	174	3.9e-14	53.3
LXL04_028283	`PF17123.12`	zf-RING_11	131	160	6.4e-10	39.3
LXL04_028283	`PF13923.13`	zf-C3HC4_2	132	173	5.5e-06	26.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9ZV53`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL49	48.624%	Swiss-Prot	moderate database homology
`Q940Q4`	Arabidopsis thaliana	RING-H2 finger protein ATL13	50.211%	Swiss-Prot	strong database homology
`Q9FL07`	Arabidopsis thaliana	RING-H2 finger protein ATL46	40.779%	Swiss-Prot	moderate database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	37.569%	Swiss-Prot	moderate database homology
`Q9FHG8`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL50	57.447%	Swiss-Prot	weak database homology

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