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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_009758
Reference: OH-1004 Chr: Chr02 Coordinates: 132804942-132806307 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1212 bp · LXL04_009758|LXL04_009758|OH1004|cDNA

ATGCTGTCTGCTTCGAATCGCTTGAAATTAGTGGTAGTTCCCCGATGGAAAACCCCCCATTTGATGTGCGTTAATTCCTTCTTATCCAATAGTTGCAGCAATCCGAGTTATGATCGTGGTCAATCTAATTTCTCTCCGAAGGTACTACATATTTATATCACATCAACCCCAGTTAAGCTTCCATGGATACATCCACTATCCTCCATGCTAAAAACCTGCACACTGAAACCCCGATCATTAGTAACACAAGCATCCATCAA...

CDS

Download CDS FASTA

1212 bp · LXL04_009758|LXL04_009758|OH1004|CDS

ATGCTGTCTGCTTCGAATCGCTTGAAATTAGTGGTAGTTCCCCGATGGAAAACCCCCCATTTGATGTGCGTTAATTCCTTCTTATCCAATAGTTGCAGCAATCCGAGTTATGATCGTGGTCAATCTAATTTCTCTCCGAAGGTACTACATATTTATATCACATCAACCCCAGTTAAGCTTCCATGGATACATCCACTATCCTCCATGCTAAAAACCTGCACACTGAAACCCCGATCATTAGTAACACAAGCATCCATCAA...

Protein

Download Protein FASTA

403 aa · LXL04_009758|LXL04_009758|OH1004|PROTEIN

MLSASNRLKLVVVPRWKTPHLMCVNSFLSNSCSNPSYDRGQSNFSPKVLHIYITSTPVKLPWIHPLSSMLKTCTLKPRSLVTQASINDEELAHQIFNKITSDSQKTANSITDLCTNHTNKLCKSKNLQAAIKLLQLLLNTSTINPIEILPSYNLLLNAASENNKTEIAANIFKDMYINNLPMDSTTYFHTTKAISKSNDLSFISSFLQEISDINPTRDVTVFNRIIYGFAECGHVHNAILVFDNIKSLKCKPNLITYNTV...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_009758
TK1151 IDTkA03G469400
OH-1004 IDLXL04_009758
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)100.000
Protein coverage (%)TK1151 63.524 / OH-1004 63.524
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_009758
LocationChr02:132804942-132806307 (+)
DescriptionSimilar to At1g11900: Pentatricopeptide repeat-containing protein At1g11900
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g11900 Pentatricopeptide repeat-containing protein At1g11900. No verified direct reference in this release
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release
At4g31850 Plays a role in the stabilization of the primary polycistronic transcript of the petL operon encoding subunits of the cytochrome b6-f complex.
PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02035.x
At2g31400 Involved in nuclear gene expression via the retrograde plastid-to-nucleus signaling.
Signals from chloroplasts converge to regulate nuclear gene expression.2007 · PMID: 17395793
Plastid signals that affect photomorphogenesis in Arabidopsis thaliana are dependent on GENOMES UNCOUPLED 1 and cryptochrome 1.2009 · DOI: 10.1111/j.1469-8137.2008.02729.x
The Arabidopsis plastid-signalling mutant gun1 (genomes uncoupled1) shows altered sensitivity to sucrose and abscisic acid and alterations in early seedling development.2010 · DOI: 10.1093/jxb/erq186
Timing the switch to phototrophic growth: a possible role of GUN1.2011 · DOI: 10.4161/psb.6.4.14900
At5g39710 Pentatricopeptide repeat-containing protein At5g39710. 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_009758 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0005737 cytoplasm Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G11900
ath:AT5G02860
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.

Mitochondrion0.713
Rank 1 · LXL04_009758 · OH-1004
Plastid0.150
Rank 2 · LXL04_009758 · OH-1004
Nucleus0.059
Rank 3 · LXL04_009758 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_009758 · OH-1004
Cell membrane0.008
Rank 5 · LXL04_009758 · 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.

PF29070.1MSC6_N121-306 aa
PF13041.13PPR_2151-187 aa
PF13812.13PPR_3209-266 aa
PF13041.13PPR_2218-261 aa
PF17177.11PPR_long235-358 aa
PF12854.14PPR_1250-281 aa
PF13041.13PPR_2252-299 aa
PF01535.27PPR255-282 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009758PF29070.1MSC6_N1213061.6e-1661.1
LXL04_009758PF13041.13PPR_21511871.4e-40137.8
LXL04_009758PF13812.13PPR_32092665.8e-2794.3
LXL04_009758PF13041.13PPR_22182611.4e-40137.8
LXL04_009758PF17177.11PPR_long2353588.4e-1142.4
LXL04_009758PF12854.14PPR_12502811.7e-2589.1
LXL04_009758PF13041.13PPR_22522991.4e-40137.8
LXL04_009758PF01535.27PPR2552822.9e-29100.0
LXL04_009758PF29070.1MSC6_N2563481.6e-1661.1
LXL04_009758PF13041.13PPR_22873341.4e-40137.8
LXL04_009758PF23276.3TPR_242943874.2e-1763.0
LXL04_009758PF13812.13PPR_33113565.8e-2794.3
LXL04_009758PF12854.14PPR_13193511.7e-2589.1
LXL04_009758PF13041.13PPR_23253691.4e-40137.8
LXL04_009758PF01535.27PPR3263522.9e-29100.0
LXL04_009758PF13812.13PPR_33453875.8e-2794.3

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
Q5BIV3Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1190037.500%Swiss-Protmoderate database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286025.316%Swiss-Protweak database homology
Q9SZ52Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g31850, chloroplastic26.220%Swiss-Protweak database homology
Q9SIC9Arabidopsis thalianaPentatricopeptide repeat-containing protein GUN1, chloroplastic27.600%Swiss-Protweak database homology
Q9FIX3Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g3971029.688%Swiss-Protweak database homology

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