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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_013252
Reference: OH-1004 Chr: Chr03 Coordinates: 26615972-26618014 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2043 bp · LXL04_013252|LXL04_013252|OH1004|cDNA

ATGCAAGCTCTGAGTGTATGGCCAACAAACACTGATATTTTCTTGAACCTTGACTCCGCCCCTCATTTTGTGGGGAGAAAAGGTAGAAACCCTAGTATTTCGAGGGGTTTTAGAAGTAGGTTTGGTTTCAGGGAGACGAGTGATGATTTACGACATGGCGTACCTTGCAGATGCTCTCGAGTTAATCGTCATGTGTTTTGGCGGCCAAAGAAGCGTTCATTTTGTTCGTCAGTTGTCCCCTTGGCTTTGGCATTTGAAGA...

CDS

Download CDS FASTA

2043 bp · LXL04_013252|LXL04_013252|OH1004|CDS

ATGCAAGCTCTGAGTGTATGGCCAACAAACACTGATATTTTCTTGAACCTTGACTCCGCCCCTCATTTTGTGGGGAGAAAAGGTAGAAACCCTAGTATTTCGAGGGGTTTTAGAAGTAGGTTTGGTTTCAGGGAGACGAGTGATGATTTACGACATGGCGTACCTTGCAGATGCTCTCGAGTTAATCGTCATGTGTTTTGGCGGCCAAAGAAGCGTTCATTTTGTTCGTCAGTTGTCCCCTTGGCTTTGGCATTTGAAGA...

Protein

Download Protein FASTA

680 aa · LXL04_013252|LXL04_013252|OH1004|PROTEIN

MQALSVWPTNTDIFLNLDSAPHFVGRKGRNPSISRGFRSRFGFRETSDDLRHGVPCRCSRVNRHVFWRPKKRSFCSSVVPLALAFEEQVVVDKPDSNSDGENKREDEKSLGETKEKRVNTRELAWSLRDAKTAEDVEMVLGDKSDLPLQVYSSMIRGFGKDKRVNSAMALVNWLKVKKHDSKSPPGPNLFIYNSLLGAMKQAEEFNHVDKIMEDMALEGVSPNVVTYNTLMGIHLAQGHEAKALELFKEIQTKGLSPSPA...

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.

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ID Mapping

Input IDLXL04_013252
TK1151 IDTkAUNG088770
OH-1004 IDLXL04_013252
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)100.000
Protein coverage (%)TK1151 70.203 / OH-1004 71.029
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 versionOH-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 IDLXL04_013252
LocationChr03:26615972-26618014 (-)
DescriptionSimilar to LPE1: Protein LOW PHOTOSYNTHETIC EFFICIENCY 1, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g46610 Required for light-regulated photosystem II (PSII) biogenesis and grana thylakoids formation by binding to the 5' UTR of PSII subunit mRNAs (e.g. psbJ, psbN and psbA) in a light-dependent manner through a redox-based mechanism, and facilitating the association of HCF173 with target mRNAs, which encodes PSII reaction center proteins (e.g. J, N and D1), thus regulating its expression by modulating ribosome loading.
LOW PHOTOSYNTHETIC EFFICIENCY 1 is required for light-regulated photosystem II biogenesis in Arabidopsis.2018 · DOI: 10.1073/pnas.1807364115
The Arabidopsis pentatricopeptide repeat protein LPE1 and its maize ortholog are required for translation of the chloroplast psbJ RNA.2019 · DOI: 10.1111/tpj.14308
At1g63080 Pentatricopeptide repeat-containing protein At1g63080, mitochondrial. No verified direct reference in this release
At1g62930 Pentatricopeptide repeat-containing protein At1g62930, chloroplastic. No verified direct reference in this release
At1g09900 Pentatricopeptide repeat-containing protein At1g09900. 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_013252 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0006413 translational initiation Biological Process
GO:0009416 response to light stimulus Biological Process
GO:0010207 photosystem II assembly Biological Process
GO:0032544 plastid translation Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0009535 chloroplast thylakoid membrane Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008494 translation activator activity Molecular Function
KEGG gene cross-reference
ath:AT1G62930
ath:AT1G63080
ath:AT3G46610
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.

Plastid0.805
Rank 1 · LXL04_013252 · OH-1004
Mitochondrion0.126
Rank 2 · LXL04_013252 · OH-1004
Nucleus0.046
Rank 3 · LXL04_013252 · OH-1004
Cytoplasm0.015
Rank 4 · LXL04_013252 · OH-1004
Cell membrane0.010
Rank 5 · LXL04_013252 · 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.

PF13041.13PPR_2187-231 aa
PF13812.13PPR_3187-233 aa
PF17177.11PPR_long203-275 aa
PF13812.13PPR_3210-267 aa
PF13041.13PPR_2222-266 aa
PF17177.11PPR_long352-506 aa
PF13041.13PPR_2389-429 aa
PF13812.13PPR_3451-509 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_013252PF13041.13PPR_21872313.1e-58194.4
LXL04_013252PF13812.13PPR_31872332.9e-41140.1
LXL04_013252PF17177.11PPR_long2032754.3e-2795.6
LXL04_013252PF13812.13PPR_32102672.9e-41140.1
LXL04_013252PF13041.13PPR_22222663.1e-58194.4
LXL04_013252PF17177.11PPR_long3525064.3e-2795.6
LXL04_013252PF13041.13PPR_23894293.1e-58194.4
LXL04_013252PF13812.13PPR_34515092.9e-41140.1
LXL04_013252PF17177.11PPR_long4656294.3e-2795.6
LXL04_013252PF13041.13PPR_24675093.1e-58194.4
LXL04_013252PF23276.3TPR_244695924.1e-1659.8
LXL04_013252PF29070.1MSC6_N4795576.1e-1762.5
LXL04_013252PF13041.13PPR_24975413.1e-58194.4
LXL04_013252PF13812.13PPR_35275802.9e-41140.1
LXL04_013252PF13812.13PPR_35556162.9e-41140.1
LXL04_013252PF13041.13PPR_25686163.1e-58194.4

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.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9SNB7Arabidopsis thalianaProtein LOW PHOTOSYNTHETIC EFFICIENCY 1, chloroplastic55.935%Swiss-Protstrong database homology
Q9CAN5Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g63080, mitochondrial21.682%Swiss-Protweak database homology
Q9LQ14Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g62930, chloroplastic23.121%Swiss-Protweak database homology
Q3EDF8Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g0990021.331%Swiss-Protweak database homology

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