RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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_033199
Reference: OH-1004 Chr: Chr07 Coordinates: 38120569-38123710 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3051 bp · LXL04_033199|LXL04_033199|OH1004|cDNA

ATGAGCAGAAACTGGGTAAAGATTAACCTCCATCAATCGAAGCAACGTTCTTCGTCATTCGCTCGTTTAATTTCTCTAATAGCGTACCCTACTTCATCGAAAGTTTCCCGCCAAAGTTCAGTTCATAACACCTTCAACAAATCCATCAGCACTTCCTCTCCTGATCAATTAGAGGGATTGATCGATTCAAATTTTAATCCTCCAGGGATCAGTTCGGACCCTCTAAGGGATTCTGGAATCTCGGTCAATTTGGGAGAAGA...

CDS

Download CDS FASTA

3051 bp · LXL04_033199|LXL04_033199|OH1004|CDS

ATGAGCAGAAACTGGGTAAAGATTAACCTCCATCAATCGAAGCAACGTTCTTCGTCATTCGCTCGTTTAATTTCTCTAATAGCGTACCCTACTTCATCGAAAGTTTCCCGCCAAAGTTCAGTTCATAACACCTTCAACAAATCCATCAGCACTTCCTCTCCTGATCAATTAGAGGGATTGATCGATTCAAATTTTAATCCTCCAGGGATCAGTTCGGACCCTCTAAGGGATTCTGGAATCTCGGTCAATTTGGGAGAAGA...

Protein

Download Protein FASTA

1016 aa · LXL04_033199|LXL04_033199|OH1004|PROTEIN

MSRNWVKINLHQSKQRSSSFARLISLIAYPTSSKVSRQSSVHNTFNKSISTSSPDQLEGLIDSNFNPPGISSDPLRDSGISVNLGEEVAVLQRSLSVDKFESRKYSDAHIICKAITENNADFSDKTQKFLSKFRAKLSESLVVDVLKSLQNAELSVKFFIWVGRQIGYNHTLPVYETLLDIMGCNNSDRIPDHFLREIKDDDDKEVLGKLLNVLIRKYCQNGSWNSALEELARLKDFGHKPSRVTYNALIQVFLEANKLD...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_033199
TK1151 IDTkA08G240590
OH-1004 IDLXL04_033199
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)97.500
Protein coverage (%)TK1151 99.901 / OH-1004 99.114
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_033199
LocationChr07:38120569-38123710 (-)
DescriptionSimilar to At1g06710: Pentatricopeptide repeat-containing protein At1g06710, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g06710 Pentatricopeptide repeat-containing protein At1g06710, mitochondrial. No verified direct reference in this release
At3g06920 Pentatricopeptide repeat-containing protein At3g06920. No verified direct reference in this release
At5g65560 Pentatricopeptide repeat-containing protein At5g65560. No verified direct reference in this release
At1g62910 Pentatricopeptide repeat-containing protein At1g62910. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
UniProt: Q76C99 Reduces the expression of the cytoplasmic male sterility (CMS)-associated mitochondrial gene ORF79, encoding a cytotoxic peptide. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_033199 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006396 RNA processing Biological Process
GO:0007005 mitochondrion organization Biological Process
GO:0044528 regulation of mitochondrial mRNA stability Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0031966 mitochondrial membrane Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G06710
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.

Mitochondrion0.788
Rank 1 · LXL04_033199 · OH-1004
Plastid0.122
Rank 2 · LXL04_033199 · OH-1004
Nucleus0.062
Rank 3 · LXL04_033199 · OH-1004
Cytoplasm0.037
Rank 4 · LXL04_033199 · OH-1004
Cell membrane0.013
Rank 5 · LXL04_033199 · 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_2212-252 aa
PF13812.13PPR_3212-253 aa
PF13041.13PPR_2241-290 aa
PF13041.13PPR_2308-356 aa
PF13812.13PPR_3343-390 aa
PF12854.14PPR_1375-405 aa
PF13041.13PPR_2382-426 aa
PF01535.27PPR382-411 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_033199PF13041.13PPR_22122521.2e-146477.4
LXL04_033199PF13812.13PPR_32122535.1e-70232.2
LXL04_033199PF13041.13PPR_22412901.2e-146477.4
LXL04_033199PF13041.13PPR_23083561.2e-146477.4
LXL04_033199PF13812.13PPR_33433905.1e-70232.2
LXL04_033199PF12854.14PPR_13754054.1e-132430.3
LXL04_033199PF13041.13PPR_23824261.2e-146477.4
LXL04_033199PF01535.27PPR3824112.9e-111356.9
LXL04_033199PF17177.11PPR_long3915405.2e-42144.3
LXL04_033199PF13041.13PPR_24655021.2e-146477.4
LXL04_033199PF23276.3TPR_244705853.7e-37127.9
LXL04_033199PF29070.1MSC6_N4706209.2e-30104.7
LXL04_033199PF13812.13PPR_34785365.1e-70232.2
LXL04_033199PF12854.14PPR_14855184.1e-132430.3
LXL04_033199PF13041.13PPR_24895381.2e-146477.4
LXL04_033199PF01535.27PPR4925222.9e-111356.9

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
Q9M9X9Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g06710, mitochondrial55.646%Swiss-Protstrong database homology
Q9M907Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0692026.781%Swiss-Protweak database homology
Q9LSL9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g6556028.343%Swiss-Protweak database homology
Q9LQ16Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g6291027.597%Swiss-Protweak database homology
Q76C99Oryza sativa subsp. indicaProtein Rf1, mitochondrial27.137%Swiss-Protweak database homology

JBrowse

View in Genome Browser