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_004021
Reference: OH-1004 Chr: Chr01 Coordinates: 122190676-122192752 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2013 bp · LXL04_004021|LXL04_004021|OH1004|cDNA

ATGAAAGCCCTCCGTCTTCTGTTTACAAACACCAAAAACCGCTCTCCCGCCAAGAAACCTTCCATTGCTCCGCTCTTCACCGACGAAACCCAATTCATCTCGCTAATCCACGCCTCCAAGACCATCAAACACCTCCAACAAATCCACGCCCAAATCATTCTCCACCAACAGTTCTCAAACACCCGAATCGTCACCCAGTTAATTTCTTCCGCTTCTTTTAAAAATAACTTCATCAACTACGCCCTTTCGATCTTCCGCCA...

CDS

Download CDS FASTA

2013 bp · LXL04_004021|LXL04_004021|OH1004|CDS

ATGAAAGCCCTCCGTCTTCTGTTTACAAACACCAAAAACCGCTCTCCCGCCAAGAAACCTTCCATTGCTCCGCTCTTCACCGACGAAACCCAATTCATCTCGCTAATCCACGCCTCCAAGACCATCAAACACCTCCAACAAATCCACGCCCAAATCATTCTCCACCAACAGTTCTCAAACACCCGAATCGTCACCCAGTTAATTTCTTCCGCTTCTTTTAAAAATAACTTCATCAACTACGCCCTTTCGATCTTCCGCCA...

Protein

Download Protein FASTA

670 aa · LXL04_004021|LXL04_004021|OH1004|PROTEIN

MKALRLLFTNTKNRSPAKKPSIAPLFTDETQFISLIHASKTIKHLQQIHAQIILHQQFSNTRIVTQLISSASFKNNFINYALSIFRHSKNPNLYLFNSLIRALADNSYYMSSISYFLLMLRSGIHPDRLTFSFFLKSTSALQEGWLGMQIHSQISKLGLLYDRFVLFSLVDMYAKVGLLENASQLFDESSQSEYQSQSTLLWNALIDGFCKSGNCSKAFELFENMPEKYDSTWSILINGLMKAGEINTAMELWHSMEEKN...

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_004021
TK1151 IDTkA01G212110
OH-1004 IDLXL04_004021
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.600
Protein coverage (%)TK1151 100.000 / OH-1004 100.000
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_004021
LocationChr01:122190676-122192752 (-)
DescriptionSimilar to PCMP-H64: Pentatricopeptide repeat-containing protein At1g04840
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g04840 Pentatricopeptide repeat-containing protein At1g04840. No verified direct reference in this release
At3g08820 Putative pentatricopeptide repeat-containing protein At3g08820. No verified direct reference in this release
At5g06540 Pentatricopeptide repeat-containing protein At5g06540. No verified direct reference in this release
At4g37380 Plays a major role in single RNA editing events in chloroplasts. No verified direct reference in this release
At1g74630 Pentatricopeptide repeat-containing protein At1g74630. 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_004021 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:1900865 chloroplast RNA modification 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:AT1G04840
ath:AT1G74630
ath:AT3G08820
ath:AT4G37380
ath:AT5G06540
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.

Mitochondrion0.648
Rank 1 · LXL04_004021 · OH-1004
Plastid0.179
Rank 2 · LXL04_004021 · OH-1004
Nucleus0.064
Rank 3 · LXL04_004021 · OH-1004
Cytoplasm0.040
Rank 4 · LXL04_004021 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_004021 · 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.

PF29070.1MSC6_N165-254 aa
PF13041.13PPR_2199-228 aa
PF01535.27PPR202-228 aa
PF12854.14PPR_1202-225 aa
PF01535.27PPR231-261 aa
PF13041.13PPR_2232-261 aa
PF12854.14PPR_1232-257 aa
PF17177.11PPR_long237-359 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_004021PF29070.1MSC6_N1652543.8e-1866.5
LXL04_004021PF13041.13PPR_21992283.1e-53178.4
LXL04_004021PF01535.27PPR2022286.9e-56183.4
LXL04_004021PF12854.14PPR_12022258.3e-37125.3
LXL04_004021PF01535.27PPR2312616.9e-56183.4
LXL04_004021PF13041.13PPR_22322613.1e-53178.4
LXL04_004021PF12854.14PPR_12322578.3e-37125.3
LXL04_004021PF17177.11PPR_long2373591e-1248.6
LXL04_004021PF13041.13PPR_22593073.1e-53178.4
LXL04_004021PF01535.27PPR2622926.9e-56183.4
LXL04_004021PF13041.13PPR_23614083.1e-53178.4
LXL04_004021PF01535.27PPR3643936.9e-56183.4
LXL04_004021PF17177.11PPR_long3674601e-1248.6
LXL04_004021PF29070.1MSC6_N3794583.8e-1866.5
LXL04_004021PF13812.13PPR_33864446.3e-2278.2
LXL04_004021PF20431.5E_motif4785402.1e-2279.9

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
Q9MAT2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g0484049.107%Swiss-Protmoderate database homology
Q9SR82Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g0882038.081%Swiss-Protmoderate database homology
Q9FG16Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0654037.364%Swiss-Protmoderate database homology
Q9SZT8Arabidopsis thalianaPentatricopeptide repeat-containing protein ELI1, chloroplastic37.656%Swiss-Protmoderate database homology
Q9CA54Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g7463036.916%Swiss-Protmoderate database homology

JBrowse

View in Genome Browser