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_005619
Reference: OH-1004 Chr: Chr01 Coordinates: 169409854-169411989 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2136 bp · LXL04_005619|LXL04_005619|OH1004|cDNA

ATGCCTCCCCAACCAGCGCCGCCAACCACCATACCCAAAAACCTAAACTTGTTCAATAGATATCGCAAAGCCAGCCAAAACCGCCCCACAGTCCGTGGTGGGTTTTTCCCCAATCAAAATCAGCAACCCACCGCGGCCGATTTCGATCTTTCAAAATGGAATCCAGAGCAATCTATTATCTCCACCCCATCACCACAACAACATTACTTCTCCGTGGCCCAAACGCTTTCTCCCATCGCTCGTTACATAGTCGATTCCTT...

CDS

Download CDS FASTA

2136 bp · LXL04_005619|LXL04_005619|OH1004|CDS

ATGCCTCCCCAACCAGCGCCGCCAACCACCATACCCAAAAACCTAAACTTGTTCAATAGATATCGCAAAGCCAGCCAAAACCGCCCCACAGTCCGTGGTGGGTTTTTCCCCAATCAAAATCAGCAACCCACCGCGGCCGATTTCGATCTTTCAAAATGGAATCCAGAGCAATCTATTATCTCCACCCCATCACCACAACAACATTACTTCTCCGTGGCCCAAACGCTTTCTCCCATCGCTCGTTACATAGTCGATTCCTT...

Protein

Download Protein FASTA

711 aa · LXL04_005619|LXL04_005619|OH1004|PROTEIN

MPPQPAPPTTIPKNLNLFNRYRKASQNRPTVRGGFFPNQNQQPTAADFDLSKWNPEQSIISTPSPQQHYFSVAQTLSPIARYIVDSFRNHRWRWGPPVVADLNKLRRVTPKLVAEVLKVQTDPIISSKFFHWAGKQNGYKHDFATYNAFAYCLNRTNQFRAADQVPDLMNMQGKPPTEKQFEILIRMHSDANRGLRVYYVYEKMKKFGVKPRVFLYNRIMDTLVKTNHLDLSMSVYNDFKDDGLVAEGITFMILIKGLCK...

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_005619
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_005619
LocationChr01:169409854-169411989 (+)
DescriptionSimilar to At4g20740: Pentatricopeptide repeat-containing protein At4g20740
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g20740 Pentatricopeptide repeat-containing protein At4g20740. No verified direct reference in this release
At3g53700 May be involved in female gametophyte development. No verified direct reference in this release
At5g64320 Pentatricopeptide repeat-containing protein At5g64320, mitochondrial. No verified direct reference in this release
At5g59900 Putative pentatricopeptide repeat-containing protein At5g59900. No verified direct reference in this release
At1g74580 Putative pentatricopeptide repeat-containing protein At1g74580. 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_005619 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0010239 chloroplast mRNA processing Biological Process
GO:0009507 chloroplast Cellular Component
GO:0042644 chloroplast nucleoid Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT3G53700
ath:AT4G20740
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.

Mitochondrion0.798
Rank 1 · LXL04_005619 · OH-1004
Plastid0.122
Rank 2 · LXL04_005619 · OH-1004
Nucleus0.063
Rank 3 · LXL04_005619 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_005619 · OH-1004
Cell membrane0.012
Rank 5 · LXL04_005619 · 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.

PF17177.11PPR_long160-277 aa
PF13041.13PPR_2211-260 aa
PF23276.3TPR_24219-343 aa
PF12854.14PPR_1246-275 aa
PF13041.13PPR_2249-290 aa
PF01535.27PPR249-276 aa
PF13041.13PPR_2280-329 aa
PF29070.1MSC6_N295-446 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_005619PF17177.11PPR_long1602774.4e-2176.0
LXL04_005619PF13041.13PPR_22112605.8e-61203.1
LXL04_005619PF23276.3TPR_242193432.7e-2279.8
LXL04_005619PF12854.14PPR_12462751e-45153.9
LXL04_005619PF13041.13PPR_22492905.8e-61203.1
LXL04_005619PF01535.27PPR2492761.3e-46154.3
LXL04_005619PF13041.13PPR_22803295.8e-61203.1
LXL04_005619PF29070.1MSC6_N2954468.1e-2072.0
LXL04_005619PF17177.11PPR_long2964254.4e-2176.0
LXL04_005619PF13041.13PPR_23163485.8e-61203.1
LXL04_005619PF12854.14PPR_13163441e-45153.9
LXL04_005619PF01535.27PPR3193471.3e-46154.3
LXL04_005619PF12854.14PPR_13824101e-45153.9
LXL04_005619PF13041.13PPR_23854255.8e-61203.1
LXL04_005619PF13812.13PPR_34805358.8e-2587.3
LXL04_005619PF13041.13PPR_24905305.8e-61203.1

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
Q9SVH3Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2074056.017%Swiss-Protstrong database homology
Q9LFF1Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g53700, chloroplastic25.632%Swiss-Protweak database homology
Q9FMF6Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g64320, mitochondrial25.926%Swiss-Protweak database homology
Q9FJE6Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At5g5990023.567%Swiss-Protweak database homology
Q9CA58Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At1g7458025.308%Swiss-Protweak database homology

JBrowse

View in Genome Browser