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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_009969
Reference: OH-1004 Chr: Chr02 Coordinates: 136956150-136959007 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2478 bp · LXL04_009969|LXL04_009969|OH1004|cDNA

ATGGCATACACATACGGCTTTTGCTCTTCGCCTTCCATTTCCTTCAACCAGAGAAGCTTCAACCACCCTATAGTTTCTCAATCGAGAGCACCTCATCTCCGAATCACTCAGATTTCCTTACAAGAATCAGTTTCTGAAGTAACCCACAACTTAGATCCTAAAATTCCAACTCCATCTCCAGCGATTGATGATAAAAAGAAAAGTTATGTCTGGGTCAACCCCAAAAACCCGAAAGCTTCACACTTCAAGAAAAAATCGCA...

CDS

Download CDS FASTA

2478 bp · LXL04_009969|LXL04_009969|OH1004|CDS

ATGGCATACACATACGGCTTTTGCTCTTCGCCTTCCATTTCCTTCAACCAGAGAAGCTTCAACCACCCTATAGTTTCTCAATCGAGAGCACCTCATCTCCGAATCACTCAGATTTCCTTACAAGAATCAGTTTCTGAAGTAACCCACAACTTAGATCCTAAAATTCCAACTCCATCTCCAGCGATTGATGATAAAAAGAAAAGTTATGTCTGGGTCAACCCCAAAAACCCGAAAGCTTCACACTTCAAGAAAAAATCGCA...

Protein

Download Protein FASTA

825 aa · LXL04_009969|LXL04_009969|OH1004|PROTEIN

MAYTYGFCSSPSISFNQRSFNHPIVSQSRAPHLRITQISLQESVSEVTHNLDPKIPTPSPAIDDKKKSYVWVNPKNPKASHFKKKSHESRYTTLTNIAEALNSCSPAEEDVFNILDSKLGSKIGEQDGVIILNNMSNPQSARIVLKYFQERCNLDRETILYNVTLKVFRKSKDLVGAEKLFDEMLQRGITPDNFTFSTIIGCARLRSLPNKAVEWFEKMPEFGIQPDNVTYAVMIDCYGRVGNIDMALRLYDRSRTEKWR...

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_009969
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_009969
LocationChr02:136956150-136959007 (+)
DescriptionSimilar to P67: Pentatricopeptide repeat-containing protein At4g16390, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g16390 Involved in chloroplast RNA processing.
An Arabidopsis pentatricopeptide repeat protein, SUPPRESSOR OF VARIEGATION7, is required for FtsH-mediated chloroplast biogenesis.2010 · DOI: 10.1104/pp.110.164111
A var2 leaf variegation suppressor locus, SUPPRESSOR OF VARIEGATION3, encodes a putative chloroplast translation elongation factor that is important for chloroplast development in the cold.2010 · DOI: 10.1186/1471-2229-10-287
Mutation of the pentatricopeptide repeat-SMR protein SVR7 impairs accumulation and translation of chloroplast ATP synthase subunits in Arabidopsis thaliana.2013 · DOI: 10.1007/s10265-012-0527-1
At5g46580 Pentatricopeptide repeat-containing protein At5g46580, chloroplastic. No verified direct reference in this release
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

Rice

Reference gene IDPossible functionPapers / DOI
Os03g0215900 Involved in translation and accumulation of chloroplast ATP synthase subunits. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_009969 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009658 chloroplast organization Biological Process
GO:0010019 chloroplast-nucleus signaling pathway Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0031930 mitochondria-nucleus signaling pathway Biological Process
GO:0042254 ribosome biogenesis Biological Process
GO:0045727 positive regulation of translation Biological Process
GO:1901259 chloroplast rRNA processing Biological Process
GO:0009507 chloroplast Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0000166 nucleotide binding Molecular Function
GO:0003677 DNA binding Molecular Function
KEGG gene cross-reference
ath:AT2G31400
ath:AT4G16390
ath:AT5G46580
dosa:Os03g0215900
osa:4332063
zma:100191483
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.

Plastid0.867
Rank 1 · LXL04_009969 · OH-1004
Mitochondrion0.116
Rank 2 · LXL04_009969 · OH-1004
Nucleus0.048
Rank 3 · LXL04_009969 · OH-1004
Cytoplasm0.035
Rank 4 · LXL04_009969 · OH-1004
Cell membrane0.016
Rank 5 · LXL04_009969 · 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_2158-202 aa
PF13041.13PPR_2209-238 aa
PF12854.14PPR_1223-252 aa
PF01535.27PPR229-253 aa
PF17177.11PPR_long244-339 aa
PF29070.1MSC6_N257-357 aa
PF13812.13PPR_3260-309 aa
PF13041.13PPR_2262-308 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009969PF13041.13PPR_21582024.8e-61203.4
LXL04_009969PF13041.13PPR_22092384.8e-61203.4
LXL04_009969PF12854.14PPR_12232521.1e-36124.9
LXL04_009969PF01535.27PPR2292531.8e-56185.2
LXL04_009969PF17177.11PPR_long2443395.7e-2691.9
LXL04_009969PF29070.1MSC6_N2573575e-2279.2
LXL04_009969PF13812.13PPR_32603097.2e-38129.2
LXL04_009969PF13041.13PPR_22623084.8e-61203.4
LXL04_009969PF01535.27PPR2642941.8e-56185.2
LXL04_009969PF13812.13PPR_33263797.2e-38129.2
LXL04_009969PF13041.13PPR_23343794.8e-61203.4
LXL04_009969PF01535.27PPR3353641.8e-56185.2
LXL04_009969PF17177.11PPR_long3515015.7e-2691.9
LXL04_009969PF29070.1MSC6_N3544605e-2279.2
LXL04_009969PF13041.13PPR_23674124.8e-61203.4
LXL04_009969PF01535.27PPR3693961.8e-56185.2

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q8GWE0Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g16390, chloroplastic62.500%Swiss-Protstrong database homology
Q9LS25Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g46580, chloroplastic38.131%Swiss-Protmoderate database homology
Q9SIC9Arabidopsis thalianaPentatricopeptide repeat-containing protein GUN1, chloroplastic26.241%Swiss-Protweak database homology
Q10PZ4Oryza sativa subsp. japonicaPentatricopeptide repeat-containing protein ATP4 homolog, chloroplastic49.698%Swiss-Protmoderate database homology

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