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_028433
Reference: OH-1004 Chr: Chr06 Coordinates: 41716074-41719247 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3174 bp · LXL04_028433|LXL04_028433|OH1004|cDNA

ATGATTTTCTCTAAGCTCCTCAAATCCAAAAGATTCTCTACTTCTCGATCATCTTCTTCCTCTCGTCGCAACCACCAATCATTTGTGTCACTCGCTACCTTCTTGAAATGTAGTTTCAATTTATCTCTCAAACATTACAACAACTTTCTTCTTCAACTCTTCAGAACCAAAAAATTTCGATTCATCACACACTTCATATCTCAACTAAACTCCAACCATATCGAAGGAGATCATATCACAAAATCAATCTTCACAAGGGC...

CDS

Download CDS FASTA

3174 bp · LXL04_028433|LXL04_028433|OH1004|CDS

ATGATTTTCTCTAAGCTCCTCAAATCCAAAAGATTCTCTACTTCTCGATCATCTTCTTCCTCTCGTCGCAACCACCAATCATTTGTGTCACTCGCTACCTTCTTGAAATGTAGTTTCAATTTATCTCTCAAACATTACAACAACTTTCTTCTTCAACTCTTCAGAACCAAAAAATTTCGATTCATCACACACTTCATATCTCAACTAAACTCCAACCATATCGAAGGAGATCATATCACAAAATCAATCTTCACAAGGGC...

Protein

Download Protein FASTA

1057 aa · LXL04_028433|LXL04_028433|OH1004|PROTEIN

MIFSKLLKSKRFSTSRSSSSSRRNHQSFVSLATFLKCSFNLSLKHYNNFLLQLFRTKKFRFITHFISQLNSNHIEGDHITKSIFTRALLKQHNYEKAVEFINTQIRKTPTILQNQILDSLVQGFCLNQKDPERGFSVLRDYLKIDGILPSSFTFCALISSFSRQGKMDRAIEVLEVMTDEKFKYPFDNFVFSTVISGFINAGNPELAVGFYQNAAKSTALQMNIVTYTCLLSAYCRLKIFKEVSELLNSIKKDGLSVDVV...

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_028433
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_028433
LocationChr06:41716074-41719247 (+)
DescriptionSimilar to At5g57250: Pentatricopeptide repeat-containing protein At5g57250, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g57250 Pentatricopeptide repeat-containing protein At5g57250, mitochondrial. No verified direct reference in this release
At4g31850 Plays a role in the stabilization of the primary polycistronic transcript of the petL operon encoding subunits of the cytochrome b6-f complex.
PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02035.x
At1g19290 Putative pentatricopeptide repeat-containing protein At1g19290. No verified direct reference in this release
At3g06920 Pentatricopeptide repeat-containing protein At3g06920. 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_028433 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000963 mitochondrial RNA processing Biological Process
GO:0006412 translation Biological Process
GO:0008380 RNA splicing Biological Process
GO:0032544 plastid translation Biological Process
GO:0043489 RNA stabilization Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G19290
ath:AT4G31850
ath:AT5G57250
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.

Mitochondrion0.828
Rank 1 · LXL04_028433 · OH-1004
Plastid0.078
Rank 2 · LXL04_028433 · OH-1004
Nucleus0.053
Rank 3 · LXL04_028433 · OH-1004
Cytoplasm0.034
Rank 4 · LXL04_028433 · OH-1004
Cell membrane0.011
Rank 5 · LXL04_028433 · 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_N27-208 aa
PF10037.16MRP-S27119-186 aa
PF12854.14PPR_1145-178 aa
PF13041.13PPR_2149-199 aa
PF01535.27PPR152-180 aa
PF13812.13PPR_3218-263 aa
PF13041.13PPR_2223-260 aa
PF01535.27PPR225-255 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_028433PF29070.1MSC6_N272087.7e-31108.3
LXL04_028433PF10037.16MRP-S271191867.4e-1452.2
LXL04_028433PF12854.14PPR_11451781.8e-120393.0
LXL04_028433PF13041.13PPR_21491991.6e-128419.4
LXL04_028433PF01535.27PPR1521801.5e-104335.9
LXL04_028433PF13812.13PPR_32182633.4e-57191.1
LXL04_028433PF13041.13PPR_22232601.6e-128419.4
LXL04_028433PF01535.27PPR2252551.5e-104335.9
LXL04_028433PF13041.13PPR_22583051.6e-128419.4
LXL04_028433PF17177.11PPR_long2743718.2e-32111.0
LXL04_028433PF13812.13PPR_32833393.4e-57191.1
LXL04_028433PF23276.3TPR_242843362.4e-40138.2
LXL04_028433PF29070.1MSC6_N2874427.7e-31108.3
LXL04_028433PF12854.14PPR_12903171.8e-120393.0
LXL04_028433PF13041.13PPR_22933411.6e-128419.4
LXL04_028433PF01535.27PPR2953251.5e-104335.9

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
Q9LVD3Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g57250, mitochondrial38.049%Swiss-Protmoderate database homology
Q9SZ52Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g31850, chloroplastic24.269%Swiss-Protweak database homology
Q9LN69Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At1g1929027.107%Swiss-Protweak database homology
Q9M907Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0692022.868%Swiss-Protweak database homology
Q76C99Oryza sativa subsp. indicaProtein Rf1, mitochondrial26.148%Swiss-Protweak database homology

JBrowse

View in Genome Browser