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_024214
Reference: OH-1004 Chr: Chr05 Coordinates: 84692426-84694990 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2565 bp · LXL04_024214|LXL04_024214|OH1004|cDNA

ATGTTCAAGGCACTCGCCATTCCTCAGCTCTCGTTTTCCCCCAAACACTACTCTACCCAGACACACACGGTTACTTCCGTGAAAAGAACATTCTCCCACATATACCAACAATGCTCACTTCAAAAGACCCTTCATCATGGAAAAGAAGCGCATGCTCACATGATTGTATCCGGGTTCAAACCCACCATCTTCGTCACAAATTGTCTTATCCAGATGTACATAAAATGTACGAACATGGAGTACGCTCATAAAGTGTTCGA...

CDS

Download CDS FASTA

2565 bp · LXL04_024214|LXL04_024214|OH1004|CDS

ATGTTCAAGGCACTCGCCATTCCTCAGCTCTCGTTTTCCCCCAAACACTACTCTACCCAGACACACACGGTTACTTCCGTGAAAAGAACATTCTCCCACATATACCAACAATGCTCACTTCAAAAGACCCTTCATCATGGAAAAGAAGCGCATGCTCACATGATTGTATCCGGGTTCAAACCCACCATCTTCGTCACAAATTGTCTTATCCAGATGTACATAAAATGTACGAACATGGAGTACGCTCATAAAGTGTTCGA...

Protein

Download Protein FASTA

854 aa · LXL04_024214|LXL04_024214|OH1004|PROTEIN

MFKALAIPQLSFSPKHYSTQTHTVTSVKRTFSHIYQQCSLQKTLHHGKEAHAHMIVSGFKPTIFVTNCLIQMYIKCTNMEYAHKVFDRMPQRDTISWNAMVFGYAGIGLLSIAQEMFDSMPERDIVSWNTLISGYLHNGSCWKSLEVFTRIRRENVELDATTFAVVLKACLGLDDHTLGIQIHGLLIRLGFVHDVVAGSATVDMYAKCKKLNESITFFNEMPVKNWVSWSALIAGCVQNDEFLSGLKLFKNMQKEGLGVS...

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_024214
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_024214
LocationChr05:84692426-84694990 (-)
DescriptionSimilar to PCMP-E90: Pentatricopeptide repeat-containing protein At3g02330, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g02330 Involved in C-to-U editing of mitochondrial RNA.
MEF13 Requires MORF3 and MORF8 for RNA Editing at Eight Targets in Mitochondrial mRNAs in Arabidopsis thaliana.2015 · DOI: 10.1016/j.molp.2015.05.008
At4g39530 Pentatricopeptide repeat-containing protein At4g39530. No verified direct reference in this release
At3g09040 Pentatricopeptide repeat-containing protein At3g09040, mitochondrial. No verified direct reference in this release
At2g27610 Pentatricopeptide repeat-containing protein At2g27610. No verified direct reference in this release
At4g13650 Pentatricopeptide repeat-containing protein At4g13650. 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_024214 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0060090 molecular adaptor activity Molecular Function
KEGG gene cross-reference
ath:AT3G02330
ath:AT3G09040
ath:AT4G39530
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.

Mitochondrion0.690
Rank 1 · LXL04_024214 · OH-1004
Plastid0.197
Rank 2 · LXL04_024214 · OH-1004
Nucleus0.042
Rank 3 · LXL04_024214 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_024214 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_024214 · 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_2123-170 aa
PF01535.27PPR126-156 aa
PF13041.13PPR_2225-272 aa
PF01535.27PPR227-257 aa
PF13041.13PPR_2328-373 aa
PF13041.13PPR_2429-476 aa
PF01535.27PPR431-459 aa
PF13041.13PPR_2531-578 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_024214PF13041.13PPR_21231701e-91301.6
LXL04_024214PF01535.27PPR1261563.3e-83269.0
LXL04_024214PF13041.13PPR_22252721e-91301.6
LXL04_024214PF01535.27PPR2272573.3e-83269.0
LXL04_024214PF13041.13PPR_23283731e-91301.6
LXL04_024214PF13041.13PPR_24294761e-91301.6
LXL04_024214PF01535.27PPR4314593.3e-83269.0
LXL04_024214PF13041.13PPR_25315781e-91301.6
LXL04_024214PF01535.27PPR5325613.3e-83269.0
LXL04_024214PF13812.13PPR_36266778.5e-30103.4
LXL04_024214PF12854.14PPR_16296591.2e-42144.0
LXL04_024214PF13041.13PPR_26316791e-91301.6
LXL04_024214PF01535.27PPR6336623.3e-83269.0
LXL04_024214PF29070.1MSC6_N6347273.6e-1350.1
LXL04_024214PF17177.11PPR_long6507292.7e-1970.1
LXL04_024214PF20431.5E_motif7508107.9e-2278.0

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
Q9FWA6Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g02330, mitochondrial57.044%Swiss-Protstrong database homology
Q9SVA5Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3953034.223%Swiss-Protmoderate database homology
Q9SS83Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g09040, mitochondrial32.787%Swiss-Protmoderate database homology
Q9ZUW3Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2761034.667%Swiss-Protmoderate database homology
Q9SVP7Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g1365033.684%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser