LXL04_005158 | RubberDandelionOmics

Gene overview

LXL04_005158

Reference: OH-1004 Chr: Chr01 Coordinates: 156746806-156750112 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1164 bp · LXL04_005158|LXL04_005158|OH1004|cDNA

ATGTCGACGGCGGCGGCGATGTCGGCTATGGGGTTCACATCCTCTAGGGATCTCTCCAAATTCAACCCCAACATTGCGATGCAAGCCTTTCAACAACCAATTGCTCTTTCCGCCCGAACAACCGGAGCTCTCCGCCATTCTTTCTCACTGAAACACCCCCACACCCGCGAGAAGTTTCCGATATTGCTCGCGTTTTCCGGAGACGGGGACGACGGTATCGGGAATGGGAATAGTTCCGGAGGAGGCGGCGGCGGAGATGA...

CDS

Download CDS FASTA

1164 bp · LXL04_005158|LXL04_005158|OH1004|CDS

ATGTCGACGGCGGCGGCGATGTCGGCTATGGGGTTCACATCCTCTAGGGATCTCTCCAAATTCAACCCCAACATTGCGATGCAAGCCTTTCAACAACCAATTGCTCTTTCCGCCCGAACAACCGGAGCTCTCCGCCATTCTTTCTCACTGAAACACCCCCACACCCGCGAGAAGTTTCCGATATTGCTCGCGTTTTCCGGAGACGGGGACGACGGTATCGGGAATGGGAATAGTTCCGGAGGAGGCGGCGGCGGAGATGA...

Protein

Download Protein FASTA

387 aa · LXL04_005158|LXL04_005158|OH1004|PROTEIN

MSTAAAMSAMGFTSSRDLSKFNPNIAMQAFQQPIALSARTTGALRHSFSLKHPHTREKFPILLAFSGDGDDGIGNGNSSGGGGGGDDESGGSGSGGDGNEKEAFLVLAEVGRSLDSIPKDLAAAIRSGKIPGSVVQRYLELEKSPFLRWLLQFGGFKERLLADDLFLTKVGIECGVGMFTKTAAEYEKRKENFTKELEIVFADVVMAVIADFMLVFLPAPTVSLRPPIAMNAGRLAKFFYNCPDNAFQTALTGASYSFLQ...

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_005158`
TK1151 ID	TkA01G079300
OH-1004 ID	LXL04_005158
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 47.028 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005158

Location Chr01:156746806-156750112 (+)

Description Similar to RER4: Protein RETICULATA-RELATED 4, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g12470`	May play a role in leaf development.	No verified direct reference in this release
`At2g40400`	May play a role in leaf development.	Functional Redundancy and Divergence within the Arabidopsis RETICULATA-RELATED Gene Family.2013 · DOI: 10.1104/pp.113.217323
`At3g56140`	May play a role in leaf development.	Functional Redundancy and Divergence within the Arabidopsis RETICULATA-RELATED Gene Family.2013 · DOI: 10.1104/pp.113.217323
`At5g22790`	May play a role in leaf development.	Functional Redundancy and Divergence within the Arabidopsis RETICULATA-RELATED Gene Family.2013 · DOI: 10.1104/pp.113.217323
`At2g37860`	May play a role in leaf development.	The lower cell density of leaf parenchyma in the Arabidopsis thaliana mutant lcd1-1 is associated with increased sensitivity to ozone and virulent Pseudomonas syringae.2003 · DOI: 10.1046/j.1365-313x.2003.01795.x Mutations in the RETICULATA gene dramatically alter internal architecture but have little effect on overall organ shape in Arabidopsis leaves.2006 · DOI: 10.1093/jxb/erl063

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005158 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000302 response to reactive oxygen species Biological Process

GO:0008652 amino acid biosynthetic process Biological Process

GO:0009648 photoperiodism Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0015822 ornithine transport Biological Process

GO:0015995 chlorophyll biosynthetic process Biological Process

GO:0048366 leaf development Biological Process

GO:0099402 plant organ development Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT2G37860

ath:AT2G40400

ath:AT3G56140

ath:AT5G12470

ath:AT5G22790

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.

Plastid0.882

Rank 1 · LXL04_005158 · OH-1004

Mitochondrion0.102

Rank 2 · LXL04_005158 · OH-1004

Nucleus0.035

Rank 3 · LXL04_005158 · OH-1004

Cytoplasm0.023

Rank 4 · LXL04_005158 · OH-1004

Cell membrane0.011

Rank 5 · LXL04_005158 · 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.

PF11891.14RETICULATA-like158-335 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005158	`PF11891.14`	RETICULATA-like	158	335	8.4e-63	212.0

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
`Q94CJ5`	Arabidopsis thaliana	Protein RETICULATA-RELATED 4, chloroplastic	70.139%	Swiss-Prot	strong database homology
`Q9SIY5`	Arabidopsis thaliana	Protein RETICULATA-RELATED 5, chloroplastic	36.770%	Swiss-Prot	moderate database homology
`Q8RWG3`	Arabidopsis thaliana	Protein RETICULATA-RELATED 6, chloroplastic	37.113%	Swiss-Prot	moderate database homology
`Q9FGP9`	Arabidopsis thaliana	Protein RETICULATA-RELATED 1, chloroplastic	30.769%	Swiss-Prot	moderate database homology
`B9DFK5`	Arabidopsis thaliana	Protein RETICULATA, chloroplastic	31.786%	Swiss-Prot	moderate database homology

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