LXL04_013122 | RubberDandelionOmics

Gene overview

LXL04_013122

Reference: OH-1004 Chr: Chr03 Coordinates: 24424048-24425807 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1254 bp · LXL04_013122|LXL04_013122|OH1004|cDNA

ATGGCGCTTTCTTCATCAGGTTTCTTCGCTGTGAGACTCGATGAATCATCAGACGTAAGTGAATCGATATCTAAAAATCGTAGCAAAACCATGACGAAGCAATCGATTAAAGCGAAGCGGTTACATAGAAATCGGGTTTCTAATTTTTTGCGATACCCTATTTCAAGAACCTTTACCAGGATTGCGCATACAACCAAGTTAAAATCTGCTACATCCGACAATCTAGGAAAAACAGTCACGGTTGCAGAGGTTTTGGACAT...

CDS

Download CDS FASTA

1254 bp · LXL04_013122|LXL04_013122|OH1004|CDS

ATGGCGCTTTCTTCATCAGGTTTCTTCGCTGTGAGACTCGATGAATCATCAGACGTAAGTGAATCGATATCTAAAAATCGTAGCAAAACCATGACGAAGCAATCGATTAAAGCGAAGCGGTTACATAGAAATCGGGTTTCTAATTTTTTGCGATACCCTATTTCAAGAACCTTTACCAGGATTGCGCATACAACCAAGTTAAAATCTGCTACATCCGACAATCTAGGAAAAACAGTCACGGTTGCAGAGGTTTTGGACAT...

Protein

Download Protein FASTA

417 aa · LXL04_013122|LXL04_013122|OH1004|PROTEIN

MALSSSGFFAVRLDESSDVSESISKNRSKTMTKQSIKAKRLHRNRVSNFLRYPISRTFTRIAHTTKLKSATSDNLGKTVTVAEVLDIKPDLESGGGDDGNGNSPPGNGGNGGGDEGGGNEEDHDEKEFGPLMKFEEVMKVAETQGVNLPSDMLEAAKATGLRKLILTRYMELQGSGWVLAFLMKYCGVLRNRMLADPSFLFKVGTEIVIDSCCATFAEVQKRGPDFWAEFELYAADLLVGIVVDIALVGMLAPYARIGKR...

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_013122`
TK1151 ID	TkA02G516390
OH-1004 ID	LXL04_013122
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013122

Location Chr03:24424048-24425807 (+)

Description Similar to RER1: Protein RETICULATA-RELATED 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At5g12470`	May play a role in leaf development.	No verified direct reference in this release
`At3g08640`	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
`At3g08630`	May play a role in leaf development.	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_013122 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000302 response to reactive oxygen species Biological Process

GO:0009648 photoperiodism Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0015822 ornithine transport Biological Process

GO:0048366 leaf development Biological Process

GO:0099402 plant organ development Biological Process

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

GO:0009706 chloroplast inner membrane Cellular Component

KEGG gene cross-reference

ath:AT2G37860

ath:AT3G08630

ath:AT3G08640

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.

Plastid0.859

Rank 1 · LXL04_013122 · OH-1004

Mitochondrion0.129

Rank 2 · LXL04_013122 · OH-1004

Nucleus0.026

Rank 3 · LXL04_013122 · OH-1004

Cytoplasm0.021

Rank 4 · LXL04_013122 · OH-1004

Cell membrane0.011

Rank 5 · LXL04_013122 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF11891.14RETICULATA-like191-371 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013122	`PF11891.14`	RETICULATA-like	191	371	4.4e-64	216.2

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
`Q9FGP9`	Arabidopsis thaliana	Protein RETICULATA-RELATED 1, chloroplastic	73.064%	Swiss-Prot	strong database homology
`B9DFK5`	Arabidopsis thaliana	Protein RETICULATA, chloroplastic	71.186%	Swiss-Prot	strong database homology
`Q94CJ5`	Arabidopsis thaliana	Protein RETICULATA-RELATED 4, chloroplastic	29.333%	Swiss-Prot	weak database homology
`Q9C9Z2`	Arabidopsis thaliana	Protein RETICULATA-RELATED 3, chloroplastic	34.783%	Swiss-Prot	moderate database homology
`Q9C9Z3`	Arabidopsis thaliana	Protein RETICULATA-RELATED 2, chloroplastic	31.441%	Swiss-Prot	moderate database homology

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