LXL04_005494 | RubberDandelionOmics

Gene overview

LXL04_005494

Reference: OH-1004 Chr: Chr01 Coordinates: 165487940-165489327 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

906 bp · LXL04_005494|LXL04_005494|OH1004|cDNA

ATGTCACGTGCTTCTCACGCTCCCCTAATCCATTTCTCTTCCACCTGCACCTCCCTCCTCCCACTGTTACACACAGATATGGCACTCAGTACGCTTTCATCGCTACCACTTAAATCCCTAAAAATCATACCTTCTCATGTCTCCTTCAATCATCTCAACCCAAATCCTTCCTCAAAATCTATAACATGTCGATTAAATCCACAAAATGCCATTTCCACCAAAGTGTCATCGGATGTTGCAGAGAATATAGAGCCGAGGAG...

CDS

Download CDS FASTA

906 bp · LXL04_005494|LXL04_005494|OH1004|CDS

ATGTCACGTGCTTCTCACGCTCCCCTAATCCATTTCTCTTCCACCTGCACCTCCCTCCTCCCACTGTTACACACAGATATGGCACTCAGTACGCTTTCATCGCTACCACTTAAATCCCTAAAAATCATACCTTCTCATGTCTCCTTCAATCATCTCAACCCAAATCCTTCCTCAAAATCTATAACATGTCGATTAAATCCACAAAATGCCATTTCCACCAAAGTGTCATCGGATGTTGCAGAGAATATAGAGCCGAGGAG...

Protein

Download Protein FASTA

301 aa · LXL04_005494|LXL04_005494|OH1004|PROTEIN

MSRASHAPLIHFSSTCTSLLPLLHTDMALSTLSSLPLKSLKIIPSHVSFNHLNPNPSSKSITCRLNPQNAISTKVSSDVAENIEPRRWKALVSTALVAAVITFSSDMSALADLNKYEADTRGEFGIGSAAQFGSADLKKTVHVNENFRRANFTSADMRESDFSGSTFNGAYLEKAVAYKANFTGADLSDTLMDRMVLNEANLTNAILVRTVLTRSDLGRAVIEGADFSDAVLDLTQKQALCKYASGTNPVTGVSTRTSLG...

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_005494`
TK1151 ID	TkA01G042080
OH-1004 ID	LXL04_005494
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.000
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

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_005494

Location Chr01:165487940-165489327 (+)

Description Similar to TL20.3: Thylakoid lumenal protein TL20.3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g12250`	Pentapeptide repeat protein of unknown function.	No verified direct reference in this release
`At2g44920`	Thylakoid lumenal 15 kDa protein 1, chloroplastic.	No verified direct reference in this release
`At5g53490`	Thylakoid lumenal 17.4 kDa protein, chloroplastic.	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_005494 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005576 extracellular region Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009534 chloroplast thylakoid Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009536 plastid Cellular Component

GO:0009543 chloroplast thylakoid lumen Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0009579 thylakoid Cellular Component

GO:0031977 thylakoid lumen Cellular Component

KEGG gene cross-reference

ath:AT1G12250

ath:AT2G44920

ath:AT5G53490

cyt:cce_1272

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.

Plastid0.983

Rank 1 · LXL04_005494 · OH-1004

Mitochondrion0.020

Rank 2 · LXL04_005494 · OH-1004

Nucleus0.012

Rank 3 · LXL04_005494 · OH-1004

Cytoplasm0.010

Rank 4 · LXL04_005494 · OH-1004

Cell membrane0.009

Rank 5 · LXL04_005494 · 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.

PF00805.29Pentapeptide130-169 aa

PF13576.13Pentapeptide_3147-175 aa

PF13576.13Pentapeptide_3147-190 aa

PF00805.29Pentapeptide155-192 aa

PF13599.14Pentapeptide_4161-233 aa

PF00805.29Pentapeptide197-232 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005494	`PF00805.29`	Pentapeptide	130	169	9.7e-22	76.9
LXL04_005494	`PF13576.13`	Pentapeptide_3	147	175	1.3e-11	45.2
LXL04_005494	`PF13576.13`	Pentapeptide_3	147	190	1.3e-11	45.2
LXL04_005494	`PF00805.29`	Pentapeptide	155	192	9.7e-22	76.9
LXL04_005494	`PF13599.14`	Pentapeptide_4	161	233	2.6e-07	31.3
LXL04_005494	`PF00805.29`	Pentapeptide	197	232	9.7e-22	76.9

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
`Q8H1Q1`	Arabidopsis thaliana	Thylakoid lumenal protein TL20.3, chloroplastic	69.366%	Swiss-Prot	strong database homology
`O22160`	Arabidopsis thaliana	Thylakoid lumenal 15 kDa protein 1, chloroplastic	32.184%	Swiss-Prot	moderate database homology
`P81760`	Arabidopsis thaliana	Thylakoid lumenal 17.4 kDa protein, chloroplastic	26.562%	Swiss-Prot	weak database homology

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