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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_011017
Reference: OH-1004 Chr: Chr02 Coordinates: 156533728-156535557 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1830 bp · LXL04_011017|LXL04_011017|OH1004|cDNA

ATGGCAATTTCCACTTCTTCCGAGTGGTCATTAGCGTGCGTTCATTGCATCAAAAGAACCCACAAAAACCTCACCTTCAATCCGTCGATTCTTCTCTTCATCTCTCCCCCTTTCTCATCTTCTTCGAGAATCCTGATCCTTAATTCCTCCAGAAGTTTCCCACCACCAATACTAGAAGATGAGGAGTCCACTGATTCTCCCCTCATCAAAATGGACCAGGAAGTTGAAGATCGTCGAGAATCATCGGTAATCGATGAAGA...

CDS

Download CDS FASTA

1830 bp · LXL04_011017|LXL04_011017|OH1004|CDS

ATGGCAATTTCCACTTCTTCCGAGTGGTCATTAGCGTGCGTTCATTGCATCAAAAGAACCCACAAAAACCTCACCTTCAATCCGTCGATTCTTCTCTTCATCTCTCCCCCTTTCTCATCTTCTTCGAGAATCCTGATCCTTAATTCCTCCAGAAGTTTCCCACCACCAATACTAGAAGATGAGGAGTCCACTGATTCTCCCCTCATCAAAATGGACCAGGAAGTTGAAGATCGTCGAGAATCATCGGTAATCGATGAAGA...

Protein

Download Protein FASTA

609 aa · LXL04_011017|LXL04_011017|OH1004|PROTEIN

MAISTSSEWSLACVHCIKRTHKNLTFNPSILLFISPPFSSSSRILILNSSRSFPPPILEDEESTDSPLIKMDQEVEDRRESSVIDEENLNQSICSLLKDPKTEEMGFESYQKAKTVPDFKPTRSTLHNLIRYSLRLKNWNSIWSIAEDFGKFKVYPNASSCCRLITSCIRAKRFKLASHLLHILKFEKEVAILSFNAAMRSYNKLHMYSSAVNVYEIMKSSGMQLDGECYGRTMEAYLKMGKNDKVISLFKEFEKSNLEW...

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_011017
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_011017
LocationChr02:156533728-156535557 (-)
DescriptionSimilar to At5g13770: Pentatricopeptide repeat-containing protein At5g13770, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g13770 Pentatricopeptide repeat-containing protein At5g13770, chloroplastic. 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
At5g04810 May play a role in the plastid ribosome biogenesis. No verified direct reference in this release
At3g22470 Pentatricopeptide repeat-containing protein At3g22470, mitochondrial. No verified direct reference in this release
At3g16010 Pentatricopeptide repeat-containing protein At3g16010. 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_011017 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006396 RNA processing Biological Process
GO:0006397 mRNA processing Biological Process
GO:0006417 regulation of translation Biological Process
GO:0009658 chloroplast organization Biological Process
GO:0010239 chloroplast mRNA processing Biological Process
GO:0005737 cytoplasm Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0009534 chloroplast thylakoid Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0042644 chloroplast nucleoid Cellular Component
GO:0042651 thylakoid membrane Cellular Component
KEGG gene cross-reference
ath:AT3G22470
ath:AT5G13770
ath:AT5G42310
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.

Mitochondrion0.605
Rank 1 · LXL04_011017 · OH-1004
Plastid0.243
Rank 2 · LXL04_011017 · OH-1004
Nucleus0.070
Rank 3 · LXL04_011017 · OH-1004
Cytoplasm0.025
Rank 4 · LXL04_011017 · OH-1004
Cell membrane0.009
Rank 5 · LXL04_011017 · 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_N217-325 aa
PF13041.13PPR_2267-310 aa
PF01535.27PPR268-295 aa
PF29070.1MSC6_N316-463 aa
PF17177.11PPR_long351-435 aa
PF13041.13PPR_2373-417 aa
PF13812.13PPR_3392-452 aa
PF12854.14PPR_1400-431 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_011017PF29070.1MSC6_N2173253.2e-2589.8
LXL04_011017PF13041.13PPR_22673101.1e-43147.8
LXL04_011017PF01535.27PPR2682951.7e-41138.3
LXL04_011017PF29070.1MSC6_N3164633.2e-2589.8
LXL04_011017PF17177.11PPR_long3514356.7e-1968.8
LXL04_011017PF13041.13PPR_23734171.1e-43147.8
LXL04_011017PF13812.13PPR_33924524.6e-2381.8
LXL04_011017PF12854.14PPR_14004311.6e-2279.6
LXL04_011017PF13041.13PPR_24034361.1e-43147.8
LXL04_011017PF01535.27PPR4064361.7e-41138.3
LXL04_011017PF23276.3TPR_244095351.7e-1454.6
LXL04_011017PF13041.13PPR_24394751.1e-43147.8
LXL04_011017PF01535.27PPR4414711.7e-41138.3
LXL04_011017PF17177.11PPR_long4515946.7e-1968.8
LXL04_011017PF29070.1MSC6_N4535343.2e-2589.8
LXL04_011017PF13812.13PPR_34615214.6e-2381.8

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
Q66GP4Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g13770, chloroplastic49.002%Swiss-Protmoderate database homology
Q8L844Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g42310, chloroplastic24.416%Swiss-Protweak database homology
Q0WMY5Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g04810, chloroplastic22.551%Swiss-Protweak database homology
Q6NQ83Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g22470, mitochondrial24.181%Swiss-Protweak database homology
Q9LW84Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g1601023.632%Swiss-Protweak database homology

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