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_021986
Reference: OH-1004 Chr: Chr04 Coordinates: 141903311-141905317 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2007 bp · LXL04_021986|LXL04_021986|OH1004|cDNA

ATGAAAAAACTGATCGTTCTATTCTCCCAAAATCTAATTTTTATCAATGGAGGATTCATTTCTTCAGTTAGATCGCTCACACAAATCCCTATCTCTCTCCGTCTTCTCACAACCTCTACAGCAACCCAAGTTGCCTCAACCTCTGTTCCTTCATCATCATCGGAAGAAGAATTTGATATGGCTTCACACATAATCCAAGAAAAAGATCTTCTCAAAAAATCCCCAAATGGTGGACTACGTATCCTAGACCTTATCGATCA...

CDS

Download CDS FASTA

2007 bp · LXL04_021986|LXL04_021986|OH1004|CDS

ATGAAAAAACTGATCGTTCTATTCTCCCAAAATCTAATTTTTATCAATGGAGGATTCATTTCTTCAGTTAGATCGCTCACACAAATCCCTATCTCTCTCCGTCTTCTCACAACCTCTACAGCAACCCAAGTTGCCTCAACCTCTGTTCCTTCATCATCATCGGAAGAAGAATTTGATATGGCTTCACACATAATCCAAGAAAAAGATCTTCTCAAAAAATCCCCAAATGGTGGACTACGTATCCTAGACCTTATCGATCA...

Protein

Download Protein FASTA

668 aa · LXL04_021986|LXL04_021986|OH1004|PROTEIN

MKKLIVLFSQNLIFINGGFISSVRSLTQIPISLRLLTTSTATQVASTSVPSSSSEEEFDMASHIIQEKDLLKKSPNGGLRILDLIDHGYLEPDAKLYNQLLNKCTQLGRIKEGKLVHTHFMNSKFSHYLVIQNTILNMYAKCDCLDNAREVFDKMPVKDMVTWTAIITGYSQNDKPEDAILLFPQMLRLNFKPNEFTFSSLLKAAGSRTNEREGEQIYGYCLKYGYDSNVFVGSALVDMYSRYEKMSEAHFLFNQLQDKN...

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_021986
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_021986
LocationChr04:141903311-141905317 (-)
DescriptionSimilar to PCMP-H87: Pentatricopeptide repeat-containing protein At3g24000, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g24000 Pentatricopeptide repeat-containing protein At3g24000, mitochondrial. No verified direct reference in this release
At2g03880 Pentatricopeptide repeat-containing protein At2g03880, mitochondrial. No verified direct reference in this release
At3g13770 Putative pentatricopeptide repeat-containing protein At3g13770, mitochondrial. No verified direct reference in this release
At3g23330 Putative pentatricopeptide repeat-containing protein At3g23330. 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

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_021986 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G03880
ath:AT3G13770
ath:AT3G23330
ath:AT3G24000
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.

Mitochondrion0.692
Rank 1 · LXL04_021986 · OH-1004
Plastid0.215
Rank 2 · LXL04_021986 · OH-1004
Nucleus0.043
Rank 3 · LXL04_021986 · OH-1004
Cytoplasm0.032
Rank 4 · LXL04_021986 · OH-1004
Cell membrane0.007
Rank 5 · LXL04_021986 · 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_2159-204 aa
PF01535.27PPR161-190 aa
PF17177.11PPR_long234-353 aa
PF13041.13PPR_2260-307 aa
PF23276.3TPR_24260-356 aa
PF01535.27PPR262-292 aa
PF13812.13PPR_3262-306 aa
PF13812.13PPR_3357-407 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_021986PF13041.13PPR_21592041.6e-58195.3
LXL04_021986PF01535.27PPR1611901.2e-56185.8
LXL04_021986PF17177.11PPR_long2343535.8e-1452.7
LXL04_021986PF13041.13PPR_22603071.6e-58195.3
LXL04_021986PF23276.3TPR_242603564.2e-1143.6
LXL04_021986PF01535.27PPR2622921.2e-56185.8
LXL04_021986PF13812.13PPR_32623062e-2692.6
LXL04_021986PF13812.13PPR_33574072e-2692.6
LXL04_021986PF13041.13PPR_23604081.6e-58195.3
LXL04_021986PF20431.5E_motif4785401.1e-2074.4
LXL04_021986PF14432.13DYW_deaminase5766685.1e-38129.5

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
Q9LIQ7Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g24000, mitochondrial57.829%Swiss-Protstrong database homology
Q9SI53Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g03880, mitochondrial40.609%Swiss-Protmoderate database homology
Q9LIC3Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g13770, mitochondrial39.898%Swiss-Protmoderate database homology
Q9LW63Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g2333038.989%Swiss-Protmoderate database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic41.105%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser