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_005080
Reference: OH-1004 Chr: Chr01 Coordinates: 154299258-154301660 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2403 bp · LXL04_005080|LXL04_005080|OH1004|cDNA

ATGGCAGCGGCTGCAGCCTGCCGGCAGAGAACTTCCATAACCAGCACAACCTTCTACCTACAAATTTTCGAGAATTCAATTAAATCAAGTTCATTGGCTGATGCCAAGACAATTCATCAGCATTTCCTCAAGAACAATCTCAATTACAGCTCCATTGTTCTGGACAAACTCACCCGCGTCTACATCTCTTTTCACCAACTCCAGCTTGCCCACCGAGTCTTCGATCGAATTCCTTACCCAGAAAGAAAGGACAACGTATT...

CDS

Download CDS FASTA

2403 bp · LXL04_005080|LXL04_005080|OH1004|CDS

ATGGCAGCGGCTGCAGCCTGCCGGCAGAGAACTTCCATAACCAGCACAACCTTCTACCTACAAATTTTCGAGAATTCAATTAAATCAAGTTCATTGGCTGATGCCAAGACAATTCATCAGCATTTCCTCAAGAACAATCTCAATTACAGCTCCATTGTTCTGGACAAACTCACCCGCGTCTACATCTCTTTTCACCAACTCCAGCTTGCCCACCGAGTCTTCGATCGAATTCCTTACCCAGAAAGAAAGGACAACGTATT...

Protein

Download Protein FASTA

800 aa · LXL04_005080|LXL04_005080|OH1004|PROTEIN

MAAAAACRQRTSITSTTFYLQIFENSIKSSSLADAKTIHQHFLKNNLNYSSIVLDKLTRVYISFHQLQLAHRVFDRIPYPERKDNVLLWNQLIRAYAWEGPFDHATNLYNEMIQSGVTPNKYTYPFALKACSSIQDIELGKLIHDRVKSEVLDNDVYICTALVDFYSKCGLLDDARQVFDKMSNRDIVAWNAMIAGSSLHGMYHKTIKLVQEMQEVGLSPNSSTIVAILPAIGEANELIQGKTVHGFCIRRIYDNSVVVG...

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_005080
TK1151 IDTkA01G088410
OH-1004 IDLXL04_005080
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)64.100
Protein coverage (%)TK1151 95.680 / OH-1004 84.375
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_005080
LocationChr01:154299258-154301660 (+)
DescriptionSimilar to PCMP-E91: Pentatricopeptide repeat-containing protein At3g16610
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g16610 Pentatricopeptide repeat-containing protein At3g16610. No verified direct reference in this release
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
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
At4g30700 Pentatricopeptide repeat-containing protein At4g30700. No verified direct reference in this release
At5g16860 Pentatricopeptide repeat-containing protein At5g16860. 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_005080 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000963 mitochondrial RNA processing Biological Process
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:0016554 cytidine to uridine editing Biological Process
GO:0016556 mRNA modification Biological Process
GO:0048366 leaf development Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
KEGG gene cross-reference
ath:AT1G11290
ath:AT3G16610
ath:AT4G18750
ath:AT4G30700
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.

Mitochondrion0.625
Rank 1 · LXL04_005080 · OH-1004
Plastid0.226
Rank 2 · LXL04_005080 · OH-1004
Nucleus0.044
Rank 3 · LXL04_005080 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_005080 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_005080 · 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_285-131 aa
PF01535.27PPR89-117 aa
PF13041.13PPR_2185-227 aa
PF13041.13PPR_2287-336 aa
PF13041.13PPR_2388-435 aa
PF13812.13PPR_3389-426 aa
PF12854.14PPR_1389-417 aa
PF01535.27PPR391-421 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_005080PF13041.13PPR_2851313.5e-67223.0
LXL04_005080PF01535.27PPR891177.9e-59192.6
LXL04_005080PF13041.13PPR_21852273.5e-67223.0
LXL04_005080PF13041.13PPR_22873363.5e-67223.0
LXL04_005080PF13041.13PPR_23884353.5e-67223.0
LXL04_005080PF13812.13PPR_33894268.2e-2897.0
LXL04_005080PF12854.14PPR_13894172.2e-2795.2
LXL04_005080PF01535.27PPR3914217.9e-59192.6
LXL04_005080PF01535.27PPR4634897.9e-59192.6
LXL04_005080PF13041.13PPR_24905373.5e-67223.0
LXL04_005080PF01535.27PPR4925227.9e-59192.6
LXL04_005080PF20431.5E_motif6076691e-1145.6
LXL04_005080PF14432.13DYW_deaminase7088001.3e-36125.0

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
Q9LUS3Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g1661048.628%Swiss-Protmoderate database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic38.551%Swiss-Protmoderate database homology
Q9SN39Arabidopsis thalianaPentatricopeptide repeat-containing protein DOT4, chloroplastic35.907%Swiss-Protmoderate database homology
Q9SUH6Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3070034.956%Swiss-Protmoderate database homology
Q9LFL5Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g1686036.121%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser