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_002623
Reference: OH-1004 Chr: Chr01 Coordinates: 53219152-53221248 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2097 bp · LXL04_002623|LXL04_002623|OH1004|cDNA

ATGGGATCAAGCTTACCGCAAACTGAATTCTTTCATAACAATGTTATTTCTATTTACGCTACACTGGGTTACATATCTGTTGCCCgcaaggtgttcgatgaaatgcctcatAAGAATGTTGTTTCTTACAATGCCATGATCGGTTCTTATACTCGTGATGGGAAAGACAAAGAAGCTTGCAACTTGTTTTCCGACATGAGAAATCAAGGGCTGGTTCCAACTCAATTCACATATGGCAGCCTATTCTCGTGTGATTCACT...

CDS

Download CDS FASTA

2097 bp · LXL04_002623|LXL04_002623|OH1004|CDS

ATGGGATCAAGCTTACCGCAAACTGAATTCTTTCATAACAATGTTATTTCTATTTACGCTACACTGGGTTACATATCTGTTGCCCGCAAGGTGTTCGATGAAATGCCTCATAAGAATGTTGTTTCTTACAATGCCATGATCGGTTCTTATACTCGTGATGGGAAAGACAAAGAAGCTTGCAACTTGTTTTCCGACATGAGAAATCAAGGGCTGGTTCCAACTCAATTCACATATGGCAGCCTATTCTCGTGTGATTCACT...

Protein

Download Protein FASTA

698 aa · LXL04_002623|LXL04_002623|OH1004|PROTEIN

MGSSLPQTEFFHNNVISIYATLGYISVARKVFDEMPHKNVVSYNAMIGSYTRDGKDKEACNLFSDMRNQGLVPTQFTYGSLFSCDSLDPKQGICLQTVAMKSGLLFADAFVGTALLGMFGRQGYVHEAFMVFDEMPFKNLVTWNAMISLFGHQGSSDTCMLMFSDLMRTQITLSEPSFVGILTGFQSYQDLESGKQLHGLIIKFGLESSVSIANSLVKMYGKCGDNKSLAEKMFKFVPNRDILSWNTIIGVLAKGKEPIK...

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_002623
TK1151 IDTkA01G435360
OH-1004 IDLXL04_002623
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)97.800
Protein coverage (%)TK1151 100.000 / OH-1004 89.255
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_002623
LocationChr01:53219152-53221248 (-)
DescriptionSimilar to At3g58590: Pentatricopeptide repeat-containing protein At3g58590
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g58590 Pentatricopeptide repeat-containing protein At3g58590. No verified direct reference in this release
At3g09040 Pentatricopeptide repeat-containing protein At3g09040, mitochondrial. No verified direct reference in this release
At4g39530 Pentatricopeptide repeat-containing protein At4g39530. No verified direct reference in this release
At4g21300 Pentatricopeptide repeat-containing protein At4g21300. No verified direct reference in this release
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

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_002623 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0003723 RNA binding Molecular Function
KEGG gene cross-reference
ath:AT3G09040
ath:AT3G58590
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.

Mitochondrion0.725
Rank 1 · LXL04_002623 · OH-1004
Plastid0.138
Rank 2 · LXL04_002623 · OH-1004
Nucleus0.042
Rank 3 · LXL04_002623 · OH-1004
Cytoplasm0.030
Rank 4 · LXL04_002623 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_002623 · 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_238-83 aa
PF12854.14PPR_139-67 aa
PF13812.13PPR_339-82 aa
PF01535.27PPR41-71 aa
PF13041.13PPR_2241-287 aa
PF29070.1MSC6_N261-400 aa
PF13041.13PPR_2342-387 aa
PF12854.14PPR_1469-498 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_002623PF13041.13PPR_238839.9e-76250.4
LXL04_002623PF12854.14PPR_139671.2e-38131.3
LXL04_002623PF13812.13PPR_339821.9e-30105.5
LXL04_002623PF01535.27PPR41718.5e-67217.6
LXL04_002623PF13041.13PPR_22412879.9e-76250.4
LXL04_002623PF29070.1MSC6_N2614001.2e-1454.9
LXL04_002623PF13041.13PPR_23423879.9e-76250.4
LXL04_002623PF12854.14PPR_14694981.2e-38131.3
LXL04_002623PF13812.13PPR_34695181.9e-30105.5
LXL04_002623PF13041.13PPR_24705179.9e-76250.4
LXL04_002623PF01535.27PPR4734998.5e-67217.6
LXL04_002623PF01535.27PPR5465748.5e-67217.6

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
Q0WN01Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g5859046.839%Swiss-Protmoderate database homology
Q9SS83Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g09040, mitochondrial30.161%Swiss-Protmoderate database homology
Q9SVA5Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3953029.699%Swiss-Protweak database homology
Q9STE1Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2130029.041%Swiss-Protweak database homology
Q9FWA6Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g02330, mitochondrial27.778%Swiss-Protweak database homology

JBrowse

View in Genome Browser