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_004930
Reference: OH-1004 Chr: Chr01 Coordinates: 150331595-150333580 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1986 bp · LXL04_004930|LXL04_004930|OH1004|cDNA

ATGAGATTCACAAAACTTCTGCAAATTCAAATTCGACCCGCCACTGCTCAAACCATACACCACCACATCCCCAATGGACTCGACTACGCTGCATACGGCCGCCTCCTCCAACACTGCACCAACCACCGTCTCATCCGCCAAGCCAAGCTCCTCCATGCCAAACTCATCCTCTCCTCCGTCACCCTCGACAACTTCTTGGCTTCAAAGCTCATCACTTTCTACTCTAAAACCAACAACCTTTTCGAAGCCCACAGGGTGTT...

CDS

Download CDS FASTA

1986 bp · LXL04_004930|LXL04_004930|OH1004|CDS

ATGAGATTCACAAAACTTCTGCAAATTCAAATTCGACCCGCCACTGCTCAAACCATACACCACCACATCCCCAATGGACTCGACTACGCTGCATACGGCCGCCTCCTCCAACACTGCACCAACCACCGTCTCATCCGCCAAGCCAAGCTCCTCCATGCCAAACTCATCCTCTCCTCCGTCACCCTCGACAACTTCTTGGCTTCAAAGCTCATCACTTTCTACTCTAAAACCAACAACCTTTTCGAAGCCCACAGGGTGTT...

Protein

Download Protein FASTA

661 aa · LXL04_004930|LXL04_004930|OH1004|PROTEIN

MRFTKLLQIQIRPATAQTIHHHIPNGLDYAAYGRLLQHCTNHRLIRQAKLLHAKLILSSVTLDNFLASKLITFYSKTNNLFEAHRVFDEIPNKNTFSWNALIMGYSMNNNHTDTLKLFGSFLSVSSIFVKPDHYTVTCVLKALSSLGYGSSFAKTFHCYIIRNGLDCDIFVVNALITAYCRCDDVVTARTLFDLAPDKDLVSWNSMMAGYSQGGSYENCKELYLKMLDLEHLTPNEFTVISILQACAQSNDLDLGMKVHK...

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_004930
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_004930
LocationChr01:150331595-150333580 (+)
DescriptionSimilar to PCMP-E49: Pentatricopeptide repeat-containing protein At2g37310
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g37310 Pentatricopeptide repeat-containing protein At2g37310. No verified direct reference in this release
At1g20230 Pentatricopeptide repeat-containing protein At1g20230. No verified direct reference in this release
At2g29760 Involved in RNA editing event in chloroplasts.
A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
At2g22410 Pentatricopeptide repeat-containing protein At2g22410, mitochondrial. No verified direct reference in this release
At3g12770 Pentatricopeptide repeat-containing protein At3g12770. 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_004930 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0016556 mRNA modification Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G20230
ath:AT2G22410
ath:AT2G29760
ath:AT2G37310
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.

Mitochondrion0.667
Rank 1 · LXL04_004930 · OH-1004
Plastid0.153
Rank 2 · LXL04_004930 · OH-1004
Nucleus0.047
Rank 3 · LXL04_004930 · OH-1004
Cytoplasm0.034
Rank 4 · LXL04_004930 · OH-1004
Cell membrane0.005
Rank 5 · LXL04_004930 · 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_293-144 aa
PF13041.13PPR_2199-247 aa
PF01535.27PPR201-228 aa
PF01535.27PPR274-300 aa
PF12854.14PPR_1300-329 aa
PF13041.13PPR_2301-333 aa
PF01535.27PPR303-332 aa
PF13041.13PPR_2331-376 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_004930PF13041.13PPR_2931441.2e-59198.9
LXL04_004930PF13041.13PPR_21992471.2e-59198.9
LXL04_004930PF01535.27PPR2012282.7e-64209.7
LXL04_004930PF01535.27PPR2743002.7e-64209.7
LXL04_004930PF12854.14PPR_13003296.3e-35119.3
LXL04_004930PF13041.13PPR_23013331.2e-59198.9
LXL04_004930PF01535.27PPR3033322.7e-64209.7
LXL04_004930PF13041.13PPR_23313761.2e-59198.9
LXL04_004930PF01535.27PPR3343612.7e-64209.7
LXL04_004930PF29070.1MSC6_N4285291.2e-1661.5
LXL04_004930PF13041.13PPR_24334811.2e-59198.9
LXL04_004930PF23276.3TPR_244385262.3e-1247.7
LXL04_004930PF17177.11PPR_long4475311.2e-0938.5
LXL04_004930PF13812.13PPR_34565141e-2177.4
LXL04_004930PF13041.13PPR_24675031.2e-59198.9
LXL04_004930PF01535.27PPR4704952.7e-64209.7

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
Q9ZUT5Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g3731053.577%Swiss-Protstrong database homology
Q9LNU6Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g2023033.178%Swiss-Protmoderate database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic32.795%Swiss-Protmoderate database homology
Q9SJZ3Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g22410, mitochondrial32.736%Swiss-Protmoderate database homology
Q9LTV8Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g1277031.470%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser