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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_037103
Reference: OH-1004 Chr: Chr08 Coordinates: 53260660-53263626 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2744 bp · LXL04_037103|LXL04_037103|OH1004|cDNA

GGTATAGGTAGTTTGACTTCCAAAATAAAGTCATGTCTCATGTGATGTGGTTGTGTGGGTGGATATTCCAATGTAGCACCACTCCAGCTCAGCTACAAGCCACTGCGTCTCTTCCTTTCTCTTTGCCTTTTGGTCTTTTTATCTACAATCTCTCTCAAACCCTACTCACCCCCCTTATCTTGTTGGTGATGGCGTCTTCCACACCACCAACCTTGACCACCACGAAATCATATCAGAACCACCATATACAAGGCCTACAG...

CDS

Download CDS FASTA

2712 bp · LXL04_037103|LXL04_037103|OH1004|CDS

ATGTCTCATGTGATGTGGTTGTGTGGGTGGATATTCCAATGTAGCACCACTCCAGCTCAGCTACAAGCCACTGCGTCTCTTCCTTTCTCTTTGCCTTTTGGTCTTTTTATCTACAATCTCTCTCAAACCCTACTCACCCCCCTTATCTTGTTGGTGATGGCGTCTTCCACACCACCAACCTTGACCACCACGAAATCATATCAGAACCACCATATACAAGGCCTACAGAACCATCACCGCCGTACACACAATGGTCATAA...

Protein

Download Protein FASTA

903 aa · LXL04_037103|LXL04_037103|OH1004|PROTEIN

MSHVMWLCGWIFQCSTTPAQLQATASLPFSLPFGLFIYNLSQTLLTPLILLVMASSTPPTLTTTKSYQNHHIQGLQNHHRRTHNGHNPLHPSPKVSLHPPAPRNPTANKPPIPAPTTVTAGASSSLQHRNSTFAPLSSKSELAADFSGRRSTRFVSKMHFGRPKAGGSSRHSVLAEDALQQLIRCSGDDRLVESVLLNFQSKLCGSDDYNFLLRELGNRNEWSMAIQCFEFAVSRERRRTEQGKLASSMISVLGRLGKID...

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_037103
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_037103
LocationChr08:53260660-53263626 (-)
DescriptionSimilar to At2g31400: Pentatricopeptide repeat-containing protein At2g31400, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
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
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
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release
At5g42310 Required for chloroplast protein synthesis and accumulation of subunits of the thylakoid protein complexes.
CRP1 Protein: (dis)similarities between Arabidopsis thaliana and Zea mays.2017 · DOI: 10.3389/fpls.2017.00163
At1g12620 Pentatricopeptide repeat-containing protein At1g12620. 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_037103 · 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: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:AT2G31400
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.

Plastid0.793
Rank 1 · LXL04_037103 · OH-1004
Mitochondrion0.160
Rank 2 · LXL04_037103 · OH-1004
Nucleus0.069
Rank 3 · LXL04_037103 · OH-1004
Cytoplasm0.039
Rank 4 · LXL04_037103 · OH-1004
Cell membrane0.015
Rank 5 · LXL04_037103 · 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_24250-374 aa
PF17177.11PPR_long256-395 aa
PF13812.13PPR_3265-325 aa
PF13041.13PPR_2277-325 aa
PF12854.14PPR_1278-305 aa
PF01535.27PPR280-309 aa
PF29070.1MSC6_N281-357 aa
PF12854.14PPR_1308-340 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_037103PF23276.3TPR_242503742.9e-31108.8
LXL04_037103PF17177.11PPR_long2563958.4e-37127.3
LXL04_037103PF13812.13PPR_32653251.1e-74247.2
LXL04_037103PF13041.13PPR_22773251.7e-91300.9
LXL04_037103PF12854.14PPR_12783051.2e-78259.2
LXL04_037103PF01535.27PPR2803092.1e-72235.1
LXL04_037103PF29070.1MSC6_N2813571.8e-2693.8
LXL04_037103PF12854.14PPR_13083401.2e-78259.2
LXL04_037103PF13041.13PPR_23293591.7e-91300.9
LXL04_037103PF13812.13PPR_33313601.1e-74247.2
LXL04_037103PF13041.13PPR_23503921.7e-91300.9
LXL04_037103PF01535.27PPR3503802.1e-72235.1
LXL04_037103PF17177.11PPR_long3565178.4e-37127.3
LXL04_037103PF29070.1MSC6_N3664411.8e-2693.8
LXL04_037103PF13812.13PPR_33714291.1e-74247.2
LXL04_037103PF12854.14PPR_13784101.2e-78259.2

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
Q9SIC9Arabidopsis thalianaPentatricopeptide repeat-containing protein GUN1, chloroplastic60.495%Swiss-Protstrong database homology
Q9S7Q2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g74850, chloroplastic26.241%Swiss-Protweak database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286027.273%Swiss-Protweak database homology
Q8L844Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g42310, chloroplastic27.677%Swiss-Protweak database homology
Q9ASZ8Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1262026.550%Swiss-Protweak database homology

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