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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_019992
Reference: OH-1004 Chr: Chr04 Coordinates: 46621485-46623524 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2040 bp · LXL04_019992|LXL04_019992|OH1004|cDNA

ATGATCATCACTGGGTTCATAAAAGACACATATGCAGCTAGCAGAATCCTCAACTTCTCTACTGGTCAATCCTCATCTAATTATCTTCATTACTCTCGTAAAATCTTTGATTGCATCGAGAACCCAAATGGGTTTATTTATAACACCATGATGCGTGCTTACTTGCAGACAAATTATCCAAAAGAGACCATCTTTCTTTACGGTTTAATGTTAAATAACAAGAACAATGTTTATCCGGATAGCTACACTTACCCTCTACT...

CDS

Download CDS FASTA

2040 bp · LXL04_019992|LXL04_019992|OH1004|CDS

ATGATCATCACTGGGTTCATAAAAGACACATATGCAGCTAGCAGAATCCTCAACTTCTCTACTGGTCAATCCTCATCTAATTATCTTCATTACTCTCGTAAAATCTTTGATTGCATCGAGAACCCAAATGGGTTTATTTATAACACCATGATGCGTGCTTACTTGCAGACAAATTATCCAAAAGAGACCATCTTTCTTTACGGTTTAATGTTAAATAACAAGAACAATGTTTATCCGGATAGCTACACTTACCCTCTACT...

Protein

Download Protein FASTA

679 aa · LXL04_019992|LXL04_019992|OH1004|PROTEIN

MIITGFIKDTYAASRILNFSTGQSSSNYLHYSRKIFDCIENPNGFIYNTMMRAYLQTNYPKETIFLYGLMLNNKNNVYPDSYTYPLLIQACIARCSNLEGKEIHNHVVKIGFDTDVYVRNTLINMYGVCGDMTDARKVFDESPVRDSVTWNSILAVYVQTGNVEEAKLIYDQMPEKNIIASNSMIVLFGRCARVPEAYQLFINMKEKDLVSWTALISCYEQNGMHQKALIMFIKMNRIGIKTDEVAVISVLSVCAHLSVM...

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_019992
TK1151 IDTkA05G110700
OH-1004 IDLXL04_019992
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)98.200
Protein coverage (%)TK1151 98.580 / OH-1004 92.047
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_019992
LocationChr04:46621485-46623524 (+)
DescriptionSimilar to PCMP-H12: Pentatricopeptide repeat-containing protein At1g08070, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g22690 Pentatricopeptide repeat-containing protein At3g22690. No verified direct reference in this release
At1g08070 Involved in multiple sites RNA editing events in chloroplasts. No verified direct reference in this release
At2g13600 Pentatricopeptide repeat-containing protein At2g13600. No verified direct reference in this release
At2g29760 Involved in RNA editing event in chloroplasts.
A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
At5g40405 Putative pentatricopeptide repeat-containing protein At5g40405. 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_019992 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009409 response to cold Biological Process
GO:0009451 RNA modification Biological Process
GO:0009644 response to high light intensity Biological Process
GO:0010027 thylakoid membrane organization Biological Process
GO:0010182 sugar mediated signaling pathway Biological Process
GO:0010207 photosystem II assembly Biological Process
GO:0010380 regulation of chlorophyll biosynthetic process Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0048564 photosystem I assembly Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
KEGG gene cross-reference
ath:AT1G08070
ath:AT2G13600
ath:AT3G22690
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.

Mitochondrion0.591
Rank 1 · LXL04_019992 · OH-1004
Plastid0.233
Rank 2 · LXL04_019992 · OH-1004
Nucleus0.053
Rank 3 · LXL04_019992 · OH-1004
Cytoplasm0.038
Rank 4 · LXL04_019992 · OH-1004
Peroxisome0.006
Rank 5 · LXL04_019992 · 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_242-91 aa
PF13041.13PPR_2146-178 aa
PF01535.27PPR148-178 aa
PF13041.13PPR_2208-255 aa
PF01535.27PPR210-240 aa
PF13041.13PPR_2309-340 aa
PF12854.14PPR_1309-336 aa
PF01535.27PPR311-340 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_019992PF13041.13PPR_242914e-69229.2
LXL04_019992PF13041.13PPR_21461784e-69229.2
LXL04_019992PF01535.27PPR1481783.6e-74240.7
LXL04_019992PF13041.13PPR_22082554e-69229.2
LXL04_019992PF01535.27PPR2102403.6e-74240.7
LXL04_019992PF13041.13PPR_23093404e-69229.2
LXL04_019992PF12854.14PPR_13093366.5e-42141.7
LXL04_019992PF01535.27PPR3113403.6e-74240.7
LXL04_019992PF01535.27PPR3423713.6e-74240.7
LXL04_019992PF13041.13PPR_24424884e-69229.2
LXL04_019992PF01535.27PPR4454743.6e-74240.7
LXL04_019992PF12854.14PPR_15105406.5e-42141.7
LXL04_019992PF20431.5E_motif5636214.7e-1453.1
LXL04_019992PF20430.4Eplus_motif6266471.8e-0628.3

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
Q9LUJ2Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g2269033.100%Swiss-Protmoderate database homology
Q9LN01Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g08070, chloroplastic36.350%Swiss-Protmoderate database homology
Q9SIT7Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g1360034.769%Swiss-Protmoderate database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic35.200%Swiss-Protmoderate database homology
Q9FND7Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At5g4040540.292%Swiss-Protmoderate database homology

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