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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_032628
Reference: OH-1004 Chr: Chr07 Coordinates: 26486169-26489640 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1962 bp · LXL04_032628|LXL04_032628|OH1004|cDNA

ATGAGAATTGCCGATTTTAACAATGCAAATTACCTTGAAGCAACCatcAAGGATTGCAGGGTCGAGATGGCATGTAAAGTGTTCGATAGAATGCTTGAAAGAAACGTTGTTTCTTGGACGTCTCTCATGTGTGGGTACCTAAATTCAGGCAACGCCAATACCTCCTTATCACTCTTATGTCAAATGGGTGGAAGTTCGATAGTCAAGCCAAATGAGTTCACTTTTTCCACCAACTTTAAAGCTTGTGGATTCATTCGTGT...

CDS

Download CDS FASTA

1962 bp · LXL04_032628|LXL04_032628|OH1004|CDS

ATGAGAATTGCCGATTTTAACAATGCAAATTACCTTGAAGCAACCATCAAGGATTGCAGGGTCGAGATGGCATGTAAAGTGTTCGATAGAATGCTTGAAAGAAACGTTGTTTCTTGGACGTCTCTCATGTGTGGGTACCTAAATTCAGGCAACGCCAATACCTCCTTATCACTCTTATGTCAAATGGGTGGAAGTTCGATAGTCAAGCCAAATGAGTTCACTTTTTCCACCAACTTTAAAGCTTGTGGATTCATTCGTGT...

Protein

Download Protein FASTA

653 aa · LXL04_032628|LXL04_032628|OH1004|PROTEIN

MRIADFNNANYLEATIKDCRVEMACKVFDRMLERNVVSWTSLMCGYLNSGNANTSLSLLCQMGGSSIVKPNEFTFSTNFKACGFIRVPENGMQIHGWCCKTGFEWFPVVGNSMIDMYSKCGRIDAASKVFDKVPERSLITWNAMIAGYAVGHNGDKSLDLFKKMQIQGKLPDEFTFTSTLKACAGLGDINSGRQIHGYLISTGFLLSQQTIVSGSLIDLYAKCGYLQDAQKIFDQVERKSVISWTTLVVGYAQGGNLSKA...

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_032628
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_032628
LocationChr07:26486169-26489640 (-)
DescriptionSimilar to PCMP-H86: Putative pentatricopeptide repeat-containing protein At3g15130
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g15130 Putative pentatricopeptide repeat-containing protein At3g15130. No verified direct reference in this release
At4g18750 Plays a major role in single RNA editing events in chloroplasts.
Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.2013 · DOI: 10.1074/jbc.m113.485755
At4g13650 Pentatricopeptide repeat-containing protein At4g13650. No verified direct reference in this release
At4g30700 Pentatricopeptide repeat-containing protein At4g30700. No verified direct reference in this release
At3g02010 Putative pentatricopeptide repeat-containing protein At2g01510. 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_032628 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0010087 phloem or xylem histogenesis Biological Process
GO:0010305 leaf vascular tissue pattern formation Biological Process
GO:0010588 cotyledon vascular tissue pattern formation Biological Process
GO:0048366 leaf development Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT3G15130
ath:AT4G13650
ath:AT4G18750
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.

Mitochondrion0.699
Rank 1 · LXL04_032628 · OH-1004
Plastid0.167
Rank 2 · LXL04_032628 · OH-1004
Nucleus0.053
Rank 3 · LXL04_032628 · OH-1004
Cytoplasm0.034
Rank 4 · LXL04_032628 · OH-1004
Cell membrane0.007
Rank 5 · LXL04_032628 · 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_234-82 aa
PF01535.27PPR111-136 aa
PF13041.13PPR_2138-184 aa
PF01535.27PPR139-165 aa
PF13041.13PPR_2313-342 aa
PF01535.27PPR315-342 aa
PF13812.13PPR_3339-387 aa
PF13041.13PPR_2340-388 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_032628PF13041.13PPR_234821.1e-58195.9
LXL04_032628PF01535.27PPR1111361.5e-55182.4
LXL04_032628PF13041.13PPR_21381841.1e-58195.9
LXL04_032628PF01535.27PPR1391651.5e-55182.4
LXL04_032628PF13041.13PPR_23133421.1e-58195.9
LXL04_032628PF01535.27PPR3153421.5e-55182.4
LXL04_032628PF13812.13PPR_33393872.3e-1970.0
LXL04_032628PF13041.13PPR_23403881.1e-58195.9
LXL04_032628PF12854.14PPR_13403691.3e-30105.6
LXL04_032628PF01535.27PPR3433731.5e-55182.4
LXL04_032628PF29070.1MSC6_N3514387.4e-1039.2
LXL04_032628PF20431.5E_motif4585201.5e-1661.1
LXL04_032628PF14432.13DYW_deaminase5586536.9e-31106.6

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
P0C898Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g1513056.240%Swiss-Protstrong database homology
Q9SN39Arabidopsis thalianaPentatricopeptide repeat-containing protein DOT4, chloroplastic37.715%Swiss-Protmoderate database homology
Q9SVP7Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g1365038.073%Swiss-Protmoderate database homology
Q9SUH6Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3070037.519%Swiss-Protmoderate database homology
Q9S7F4Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At2g0151036.991%Swiss-Protmoderate database homology

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