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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_013338
Reference: OH-1004 Chr: Chr03 Coordinates: 28081795-28083801 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2007 bp · LXL04_013338|LXL04_013338|OH1004|cDNA

ATGAAGTACATGGATGCGTGGTCATGGACTACTACTCCCACACCTTTCATCACAATCAACCTACAGAATTCCCCGTCGACGAGTCACCGGAAAAAACTGCAGAATCGTTCAATAATCATCGTAAGTTCTAGCACCTCAATTAAAGATATATGGCGGAAGCAAACAAAGTCCACAACTCTAAGACCGTCATCTTCTCTCCAACCTTATCGTCGAAAACCAGAAACTGGTCACTTAGATCACAGCGTAGACATGGAAGAACT...

CDS

Download CDS FASTA

2007 bp · LXL04_013338|LXL04_013338|OH1004|CDS

ATGAAGTACATGGATGCGTGGTCATGGACTACTACTCCCACACCTTTCATCACAATCAACCTACAGAATTCCCCGTCGACGAGTCACCGGAAAAAACTGCAGAATCGTTCAATAATCATCGTAAGTTCTAGCACCTCAATTAAAGATATATGGCGGAAGCAAACAAAGTCCACAACTCTAAGACCGTCATCTTCTCTCCAACCTTATCGTCGAAAACCAGAAACTGGTCACTTAGATCACAGCGTAGACATGGAAGAACT...

Protein

Download Protein FASTA

668 aa · LXL04_013338|LXL04_013338|OH1004|PROTEIN

MKYMDAWSWTTTPTPFITINLQNSPSTSHRKKLQNRSIIIVSSSTSIKDIWRKQTKSTTLRPSSSLQPYRRKPETGHLDHSVDMEELVSSINQTTNEHELFALLSPYKTRQLSIRFMVTLLSRETDWQRSIALLDWINEQALYTPSVYAYNVVLRNVLRAKQWEIAYGLFDEMRQRALSADRYTYSTLITHFGKEGKFDDALSWLQKMEHDHVSGDLVVYSNLIELSRKLCDYSKAISIFSRLKQSGISPDLVAYNSMIN...

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_013338
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_013338
LocationChr03:28081795-28083801 (-)
DescriptionSimilar to At5g39980: Pentatricopeptide repeat-containing protein At5g39980, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g39980 Pentatricopeptide repeat-containing protein At5g39980, chloroplastic. No verified direct reference in this release
At1g62930 Pentatricopeptide repeat-containing protein At1g62930, chloroplastic. No verified direct reference in this release
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release
At1g62910 Pentatricopeptide repeat-containing protein At1g62910. No verified direct reference in this release
At1g63150 Pentatricopeptide repeat-containing protein At1g63150. 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_013338 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009658 chloroplast organization Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0009941 chloroplast envelope Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G62930
ath:AT5G39980
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.

Plastid0.477
Rank 1 · LXL04_013338 · OH-1004
Mitochondrion0.373
Rank 2 · LXL04_013338 · OH-1004
Nucleus0.067
Rank 3 · LXL04_013338 · OH-1004
Cytoplasm0.028
Rank 4 · LXL04_013338 · OH-1004
Cell membrane0.009
Rank 5 · LXL04_013338 · 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.

PF17177.11PPR_long112-250 aa
PF13041.13PPR_2145-193 aa
PF12854.14PPR_1178-209 aa
PF01535.27PPR183-210 aa
PF13041.13PPR_2185-224 aa
PF13812.13PPR_3205-264 aa
PF17177.11PPR_long235-317 aa
PF12854.14PPR_1247-279 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_013338PF17177.11PPR_long1122501.2e-29104.0
LXL04_013338PF13041.13PPR_21451932.9e-82271.3
LXL04_013338PF12854.14PPR_11782091.4e-51172.6
LXL04_013338PF01535.27PPR1832101.3e-73238.9
LXL04_013338PF13041.13PPR_21852242.9e-82271.3
LXL04_013338PF13812.13PPR_32052641.5e-56189.1
LXL04_013338PF17177.11PPR_long2353171.2e-29104.0
LXL04_013338PF12854.14PPR_12472791.4e-51172.6
LXL04_013338PF13041.13PPR_22502982.9e-82271.3
LXL04_013338PF01535.27PPR2532791.3e-73238.9
LXL04_013338PF13812.13PPR_32743341.5e-56189.1
LXL04_013338PF13041.13PPR_22853312.9e-82271.3
LXL04_013338PF01535.27PPR2883181.3e-73238.9
LXL04_013338PF29070.1MSC6_N2903791.3e-2074.6
LXL04_013338PF13041.13PPR_23203642.9e-82271.3
LXL04_013338PF01535.27PPR3243531.3e-73238.9

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
Q9FLD8Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g39980, chloroplastic74.125%Swiss-Protstrong database homology
Q9LQ14Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g62930, chloroplastic29.646%Swiss-Protweak database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286022.760%Swiss-Protweak database homology
Q9LQ16Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g6291028.889%Swiss-Protweak database homology
Q9CAM8Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g6315028.188%Swiss-Protweak database homology

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