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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_009612
Reference: OH-1004 Chr: Chr02 Coordinates: 129715116-129720700 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3336 bp · LXL04_009612|LXL04_009612|OH1004|cDNA

ATGGATGTGAGCTCTGTTTTCTTTGTAAAACCAAATCAACATCCATTACCGTCCTCCTTCACTTCTTGCATTTCTCCGACCATCTCCTTACGCCCGGAGTTCTTTGGCCCTGAATTTCGTCGTCCTTCTCGCCGGAAAAAATGCTGCAGCCTTGGGCTAGGGTTAGGCTTGGGGGTTCATTTTCATTCTCCGTCGATTAGAACAAAAAGGAGGACTGTCTTCAGAACATCTGCGGCTTTGGATGTGCAAACGATTGTTGT...

CDS

Download CDS FASTA

3336 bp · LXL04_009612|LXL04_009612|OH1004|CDS

ATGGATGTGAGCTCTGTTTTCTTTGTAAAACCAAATCAACATCCATTACCGTCCTCCTTCACTTCTTGCATTTCTCCGACCATCTCCTTACGCCCGGAGTTCTTTGGCCCTGAATTTCGTCGTCCTTCTCGCCGGAAAAAATGCTGCAGCCTTGGGCTAGGGTTAGGCTTGGGGGTTCATTTTCATTCTCCGTCGATTAGAACAAAAAGGAGGACTGTCTTCAGAACATCTGCGGCTTTGGATGTGCAAACGATTGTTGT...

Protein

Download Protein FASTA

1111 aa · LXL04_009612|LXL04_009612|OH1004|PROTEIN

MDVSSVFFVKPNQHPLPSSFTSCISPTISLRPEFFGPEFRRPSRRKKCCSLGLGLGLGVHFHSPSIRTKRRTVFRTSAALDVQTIVVVVSFVAVSALTVYYFNYSNKKHDDGSNKVSKPIEHTDSQQSSSIVNHTLNGQKPSVIVLQREHHDDESKDIVTEVKTIIHDIADEPAEIHSNGKVPQTISALASSGPDTIATESSDVKSSFTKDLIMLESSFKEPHNVMELSSQKSSLSMVIESGDVSCIPPSERTVVCFDEK...

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_009612
TK1151 IDTkA03G451230
OH-1004 IDLXL04_009612
Relationship / confidenceSequence Supported Annotation Or Model Conflict / Review
Protein identity (%)98.900
Protein coverage (%)TK1151 89.848 / OH-1004 47.705
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_009612
LocationChr02:129715116-129720700 (-)
DescriptionSimilar to MRL1: Pentatricopeptide repeat-containing protein MRL1, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
UniProt: Q0WLC6 Regulator of the large subunit (LS) of RuBisCO. No verified direct reference in this release
At5g39710 Pentatricopeptide repeat-containing protein At5g39710. No verified direct reference in this release
At2g15630 Pentatricopeptide repeat-containing protein At2g15630, mitochondrial. No verified direct reference in this release
At3g04760 Pentatricopeptide repeat-containing protein At3g04760, chloroplastic. No verified direct reference in this release
At5g16640 Pentatricopeptide repeat-containing protein At5g16640, mitochondrial. 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_009612 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0010239 chloroplast mRNA processing Biological Process
GO:0048255 mRNA stabilization Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003729 mRNA binding Molecular Function
GO:0048027 mRNA 5'-UTR binding Molecular Function
KEGG gene cross-reference
ath:AT4G34830
ath:AT5G39710
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.

Plastid0.921
Rank 1 · LXL04_009612 · OH-1004
Mitochondrion0.058
Rank 2 · LXL04_009612 · OH-1004
Nucleus0.054
Rank 3 · LXL04_009612 · OH-1004
Cytoplasm0.029
Rank 4 · LXL04_009612 · OH-1004
Cell membrane0.015
Rank 5 · LXL04_009612 · 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_2489-538 aa
PF29070.1MSC6_N492-580 aa
PF17177.11PPR_long494-652 aa
PF13041.13PPR_2529-573 aa
PF01535.27PPR529-557 aa
PF23276.3TPR_24534-657 aa
PF13812.13PPR_3547-608 aa
PF12854.14PPR_1556-581 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009612PF13041.13PPR_24895385e-57190.5
LXL04_009612PF29070.1MSC6_N4925802.8e-1557.0
LXL04_009612PF17177.11PPR_long4946522.4e-30106.2
LXL04_009612PF13041.13PPR_25295735e-57190.5
LXL04_009612PF01535.27PPR5295574.6e-46152.6
LXL04_009612PF23276.3TPR_245346571.3e-2590.5
LXL04_009612PF13812.13PPR_35476082.6e-47159.5
LXL04_009612PF12854.14PPR_15565812.5e-34117.4
LXL04_009612PF13041.13PPR_25635965e-57190.5
LXL04_009612PF01535.27PPR5635924.6e-46152.6
LXL04_009612PF12854.14PPR_15906222.5e-34117.4
LXL04_009612PF13041.13PPR_25946445e-57190.5
LXL04_009612PF01535.27PPR5976244.6e-46152.6
LXL04_009612PF13041.13PPR_26707115e-57190.5
LXL04_009612PF17177.11PPR_long6708222.4e-30106.2
LXL04_009612PF29070.1MSC6_N6998152.8e-1557.0

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q0WLC6Arabidopsis thalianaPentatricopeptide repeat-containing protein MRL1, chloroplastic46.221%Swiss-Protmoderate database homology
Q9FIX3Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g3971026.171%Swiss-Protweak database homology
Q9ZQF1Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g15630, mitochondrial23.077%Swiss-Protweak database homology
Q9SR00Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g04760, chloroplastic25.647%Swiss-Protweak database homology
Q9FMD3Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g16640, mitochondrial25.852%Swiss-Protweak database homology

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