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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_009607
Reference: OH-1004 Chr: Chr02 Coordinates: 129578136-129581011 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2631 bp · LXL04_009607|LXL04_009607|OH1004|cDNA

ATGACACTTTCATACCACTCCATCTCCCCAATTCTCATCCGCAGTGCAAACAAAACCACCATACAAGATTACAGTTCCCCCCAATTTACCACCCGAGGGTTCAAATTCGCCGTGCGCCGGTCAATCGTACTTTGCGAGAGCTCTCTAGCTAAACCACCCGCCTCCAGATCCAGAACCAGATCCAAACCCAAACCAAAAGAGCTGGTATTCGGCTACCCATCAAACAGCGTCGAAAAAGGCAAGTACAGCTATGAAGTTGA...

CDS

Download CDS FASTA

2631 bp · LXL04_009607|LXL04_009607|OH1004|CDS

ATGACACTTTCATACCACTCCATCTCCCCAATTCTCATCCGCAGTGCAAACAAAACCACCATACAAGATTACAGTTCCCCCCAATTTACCACCCGAGGGTTCAAATTCGCCGTGCGCCGGTCAATCGTACTTTGCGAGAGCTCTCTAGCTAAACCACCCGCCTCCAGATCCAGAACCAGATCCAAACCCAAACCAAAAGAGCTGGTATTCGGCTACCCATCAAACAGCGTCGAAAAAGGCAAGTACAGCTATGAAGTTGA...

Protein

Download Protein FASTA

876 aa · LXL04_009607|LXL04_009607|OH1004|PROTEIN

MTLSYHSISPILIRSANKTTIQDYSSPQFTTRGFKFAVRRSIVLCESSLAKPPASRSRTRSKPKPKELVFGYPSNSVEKGKYSYEVESLLNKLSGLPPRGSIARCLEPFKNKLSLNDFALVFKELAQRGDWQRSLRLFKQMQRQVWSKPNDHIYTIVIGILGREGLLDKCYEVFEEMPSEGVPRTVFSYTSIINAYGRNGQYETSLQLLDRMKKERISPNILTYNTVINSCARGGYDWEGLLSLFAEMRHEGLQPDLVTY...

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_009607
TK1151 IDTkA03G450830
OH-1004 IDLXL04_009607
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.800
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 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_009607
LocationChr02:129578136-129581011 (+)
DescriptionSimilar to PTAC2: Pentatricopeptide repeat-containing protein At1g74850, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g74850 Involved in plastid gene expression.
pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression.2006 · DOI: 10.1105/tpc.105.036392
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
At2g18940 Pentatricopeptide repeat-containing protein At2g18940, chloroplastic. No verified direct reference in this release
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. 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_009607 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0010019 chloroplast-nucleus signaling pathway Biological Process
GO:0031930 mitochondria-nucleus signaling pathway Biological Process
GO:0042793 plastid transcription Biological Process
GO:0045893 positive regulation of DNA-templated transcription Biological Process
GO:0048255 mRNA stabilization Biological Process
GO:0009507 chloroplast Cellular Component
GO:0042644 chloroplast nucleoid Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G74850
ath:AT2G18940
ath:AT2G31400
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.

Plastid0.694
Rank 1 · LXL04_009607 · OH-1004
Mitochondrion0.172
Rank 2 · LXL04_009607 · OH-1004
Nucleus0.076
Rank 3 · LXL04_009607 · OH-1004
Cytoplasm0.022
Rank 4 · LXL04_009607 · OH-1004
Cell membrane0.012
Rank 5 · LXL04_009607 · 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.

PF23276.3TPR_24104-207 aa
PF17177.11PPR_long122-226 aa
PF13041.13PPR_2149-195 aa
PF01535.27PPR153-182 aa
PF13812.13PPR_3173-231 aa
PF12854.14PPR_1181-213 aa
PF13041.13PPR_2185-233 aa
PF01535.27PPR187-216 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009607PF23276.3TPR_241042071.9e-35122.4
LXL04_009607PF17177.11PPR_long1222261.2e-33117.0
LXL04_009607PF13041.13PPR_21491952.9e-93306.5
LXL04_009607PF01535.27PPR1531823e-79256.6
LXL04_009607PF13812.13PPR_31732312.5e-65217.2
LXL04_009607PF12854.14PPR_11812137.8e-59195.8
LXL04_009607PF13041.13PPR_21852332.9e-93306.5
LXL04_009607PF01535.27PPR1872163e-79256.6
LXL04_009607PF17177.11PPR_long2243901.2e-33117.0
LXL04_009607PF13041.13PPR_22392692.9e-93306.5
LXL04_009607PF29070.1MSC6_N2423172.8e-32113.0
LXL04_009607PF13812.13PPR_32433042.5e-65217.2
LXL04_009607PF12854.14PPR_12522837.8e-59195.8
LXL04_009607PF13041.13PPR_22553022.9e-93306.5
LXL04_009607PF13812.13PPR_33143742.5e-65217.2
LXL04_009607PF13041.13PPR_23263722.9e-93306.5

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
Q9S7Q2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g74850, chloroplastic68.612%Swiss-Protstrong database homology
Q9SIC9Arabidopsis thalianaPentatricopeptide repeat-containing protein GUN1, chloroplastic26.130%Swiss-Protweak database homology
O64624Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g18940, chloroplastic26.929%Swiss-Protweak database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286024.363%Swiss-Protweak database homology

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