LXL04_007661 | RubberDandelionOmics

Gene overview

LXL04_007661

Reference: OH-1004 Chr: Chr02 Coordinates: 55527668-55531264 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1272 bp · LXL04_007661|LXL04_007661|OH1004|cDNA

ATGTCGAATCATTGGGTGTTGTGCAGCTTTCTATGTTTATTGGCTTCCGGGGTGACGGCAAATGTTGTTTTGATGGGGAATAATCTTACTTTAGCTTTTGATGACATCGAAGCTAACTTTGCTCCACCTGTGAAAGGTTCTGGGGAGTGTGGAAGGTTGTTTCTGGCAGAGCCTCTGGATGCTTGTGGAGTTTTGAGTAATAAAACAGTTAAAAGCAGCATAAAACAGGCGTTTGTTTTAATAGTTAGAGGAGGATGTAG...

CDS

Download CDS FASTA

1272 bp · LXL04_007661|LXL04_007661|OH1004|CDS

ATGTCGAATCATTGGGTGTTGTGCAGCTTTCTATGTTTATTGGCTTCCGGGGTGACGGCAAATGTTGTTTTGATGGGGAATAATCTTACTTTAGCTTTTGATGACATCGAAGCTAACTTTGCTCCACCTGTGAAAGGTTCTGGGGAGTGTGGAAGGTTGTTTCTGGCAGAGCCTCTGGATGCTTGTGGAGTTTTGAGTAATAAAACAGTTAAAAGCAGCATAAAACAGGCGTTTGTTTTAATAGTTAGAGGAGGATGTAG...

Protein

Download Protein FASTA

423 aa · LXL04_007661|LXL04_007661|OH1004|PROTEIN

MSNHWVLCSFLCLLASGVTANVVLMGNNLTLAFDDIEANFAPPVKGSGECGRLFLAEPLDACGVLSNKTVKSSIKQAFVLIVRGGCSFEDKVRRAQSAGFKAAIVYNNDDTDLVAMAGNSGGIAIHAVFVSKSSGLKLSKYAGIPSVELWIIPSYENSAWSIMAISFISLLAMSAVLATCFFVRRHRIRREHPHTSRVREFHGMSSRLVKAMPSLIFTAVLEDNCTSATCAICLEDYNVGDKLRILPCRHKFHTICVDAW...

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_007661`
TK1151 ID	TkA03G202910
OH-1004 ID	LXL04_007661
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_007661

Location Chr02:55527668-55531264 (+)

Description Similar to RMR2: Receptor homology region, transmembrane domain- and RING domain-containing protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g71980`	Involved in the trafficking of vacuolar proteins.	No verified direct reference in this release
`At1g35630`	Involved in the trafficking of vacuolar proteins.	No verified direct reference in this release
`At4g09560`	Involved in the trafficking of vacuolar proteins.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0167500`	Involved in the trafficking of vacuolar proteins.	No verified direct reference in this release
`Os08g0104300`	Involved in the trafficking of vacuolar proteins.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_007661 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0015031 protein transport Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0000326 protein storage vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0012505 endomembrane system Cellular Component

GO:0032586 protein storage vacuole membrane Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G35630

ath:AT1G71980

ath:AT4G09560

dosa:Os03g0167500

dosa:Os08g0104300

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.

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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.

Lysosome / Vacuole0.406

Rank 1 · LXL04_007661 · OH-1004

Cytoplasm0.255

Rank 2 · LXL04_007661 · OH-1004

Golgi apparatus0.211

Rank 3 · LXL04_007661 · OH-1004

Endoplasmic reticulum0.198

Rank 4 · LXL04_007661 · OH-1004

Cell membrane0.147

Rank 5 · LXL04_007661 · 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.

PF02225.28PA56-138 aa

PF13639.13zf-RING_2229-272 aa

PF17123.12zf-RING_11230-257 aa

PF00097.32zf-C3HC4230-271 aa

PF13923.13zf-C3HC4_2230-271 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007661	`PF02225.28`	PA	56	138	1.3e-14	54.8
LXL04_007661	`PF13639.13`	zf-RING_2	229	272	3.2e-13	50.4
LXL04_007661	`PF17123.12`	zf-RING_11	230	257	7.9e-11	42.2
LXL04_007661	`PF00097.32`	zf-C3HC4	230	271	2.1e-07	31.4
LXL04_007661	`PF13923.13`	zf-C3HC4_2	230	271	3.6e-06	27.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8VZ14`	Arabidopsis thaliana	Receptor homology region, transmembrane domain- and RING domain-containing protein 2	57.549%	Swiss-Prot	strong database homology
`F4HZZ5`	Arabidopsis thaliana	Receptor homology region, transmembrane domain- and RING domain-containing protein 5	52.581%	Swiss-Prot	strong database homology
`Q0WPW5`	Arabidopsis thaliana	Receptor homology region, transmembrane domain- and RING domain-containing protein 4	46.712%	Swiss-Prot	moderate database homology
`Q10R93`	Oryza sativa subsp. japonica	Receptor homology region, transmembrane domain- and RING domain-containing protein 1	58.333%	Swiss-Prot	strong database homology
`Q69U49`	Oryza sativa subsp. japonica	Receptor homology region, transmembrane domain- and RING domain-containing protein 2	56.709%	Swiss-Prot	strong database homology

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