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_013504
Reference: OH-1004 Chr: Chr03 Coordinates: 30579655-30581727 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2073 bp · LXL04_013504|LXL04_013504|OH1004|cDNA

ATGAGATGGACGAGAGGTCATTTTCGACATCTCATTGGCGGTACCGAACGAGCCATATCCACTTCTTCTGAAACCTTTTTTAGAACCCCTAATCATCAAAAAACTTTCTTTAAATCCCAAAACAGTGAAGATAATCTCGTAAAAAGACTATGCCGAGAAAACAAACATGAAGAAGCTATAATTAATCTACGTGAACGTCACCGTTTAACAGAAGCAATTCAAGTACTTGATCATATCGAACGACCTTCTCCATCAGTGTA...

CDS

Download CDS FASTA

2073 bp · LXL04_013504|LXL04_013504|OH1004|CDS

ATGAGATGGACGAGAGGTCATTTTCGACATCTCATTGGCGGTACCGAACGAGCCATATCCACTTCTTCTGAAACCTTTTTTAGAACCCCTAATCATCAAAAAACTTTCTTTAAATCCCAAAACAGTGAAGATAATCTCGTAAAAAGACTATGCCGAGAAAACAAACATGAAGAAGCTATAATTAATCTACGTGAACGTCACCGTTTAACAGAAGCAATTCAAGTACTTGATCATATCGAACGACCTTCTCCATCAGTGTA...

Protein

Download Protein FASTA

690 aa · LXL04_013504|LXL04_013504|OH1004|PROTEIN

MRWTRGHFRHLIGGTERAISTSSETFFRTPNHQKTFFKSQNSEDNLVKRLCRENKHEEAIINLRERHRLTEAIQVLDHIERPSPSVYSNLLKLCLQQKALEGTKRVHTHIKRSGFSPGLSSLNRIIDCYCKCGSLVDARIVFDEMREKDLCSWNTIISGYAKAGQLKQARNLFDEMPERDNFSWTAIISGYVRHNLPNDALHLCRTMLQDYTITFNKFTVCSALAASSATQSLMIGKEIHGHIIRTGIDSDAVVYSALSD...

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_013504
TK1151 IDTkA02G493190
OH-1004 IDLXL04_013504
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)99.500
Protein coverage (%)TK1151 75.692 / OH-1004 55.507
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_013504
LocationChr03:30579655-30581727 (-)
DescriptionSimilar to PCMP-H5: Pentatricopeptide repeat-containing protein At4g37170
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g37170 Pentatricopeptide repeat-containing protein At4g37170. No verified direct reference in this release
At2g22070 Pentatricopeptide repeat-containing protein At2g22070. No verified direct reference in this release
At4g02750 Pentatricopeptide repeat-containing protein At4g02750. No verified direct reference in this release
At3g23330 Putative pentatricopeptide repeat-containing protein At3g23330. 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_013504 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0010214 seed coat development Biological Process
GO:0140547 acquisition of seed longevity 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:AT2G22070
ath:AT4G02750
ath:AT4G37170
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.

Mitochondrion0.678
Rank 1 · LXL04_013504 · OH-1004
Plastid0.203
Rank 2 · LXL04_013504 · OH-1004
Nucleus0.046
Rank 3 · LXL04_013504 · OH-1004
Cytoplasm0.030
Rank 4 · LXL04_013504 · OH-1004
Cell membrane0.007
Rank 5 · LXL04_013504 · 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.

PF12854.14PPR_1114-146 aa
PF01535.27PPR121-149 aa
PF13041.13PPR_2149-179 aa
PF12854.14PPR_1149-176 aa
PF01535.27PPR152-179 aa
PF13041.13PPR_2281-330 aa
PF29070.1MSC6_N281-376 aa
PF01535.27PPR284-313 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_013504PF12854.14PPR_11141462.3e-44149.5
LXL04_013504PF01535.27PPR1211493e-58190.8
LXL04_013504PF13041.13PPR_21491792e-55185.4
LXL04_013504PF12854.14PPR_11491762.3e-44149.5
LXL04_013504PF01535.27PPR1521793e-58190.8
LXL04_013504PF13041.13PPR_22813302e-55185.4
LXL04_013504PF29070.1MSC6_N2813769.7e-1555.3
LXL04_013504PF01535.27PPR2843133e-58190.8
LXL04_013504PF13041.13PPR_23824292e-55185.4
LXL04_013504PF01535.27PPR3864103e-58190.8
LXL04_013504PF29070.1MSC6_N3884809.7e-1555.3
LXL04_013504PF20431.5E_motif5005621.9e-1867.1
LXL04_013504PF20430.4Eplus_motif5675945.7e-0626.7
LXL04_013504PF14432.13DYW_deaminase5986901.1e-37128.4

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
O23169Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3717060.091%Swiss-Protstrong database homology
Q9SHZ8Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2207039.730%Swiss-Protmoderate database homology
Q9SY02Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g0275040.032%Swiss-Protmoderate database homology
Q9LW63Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g2333040.879%Swiss-Protmoderate database homology
Q9LFL5Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g1686039.905%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser