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_008651
Reference: OH-1004 Chr: Chr02 Coordinates: 105196522-105198894 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2373 bp · LXL04_008651|LXL04_008651|OH1004|cDNA

ATGCTCCATGGAAGACGAAAAACAACATCACCTAACAAACCCCTTTTCCGATATCCACTTATTCGAAGCAAAACCACAATCATCAAACCCAGTACTTCCAAATCAAAACTCGGTACCTTCCTCGTCGTCGCTTCCATCGTAAAATCCCTATCTGAGCCGGGAGGTACTCGTAACTTTAACAATGGAGAATCAAGCTTGGTTTCACTCTCCGAACCACTCGTTCTTCAAATCCTTAGAAGGAGCTCTCTCGATGCATCGAA...

CDS

Download CDS FASTA

2373 bp · LXL04_008651|LXL04_008651|OH1004|CDS

ATGCTCCATGGAAGACGAAAAACAACATCACCTAACAAACCCCTTTTCCGATATCCACTTATTCGAAGCAAAACCACAATCATCAAACCCAGTACTTCCAAATCAAAACTCGGTACCTTCCTCGTCGTCGCTTCCATCGTAAAATCCCTATCTGAGCCGGGAGGTACTCGTAACTTTAACAATGGAGAATCAAGCTTGGTTTCACTCTCCGAACCACTCGTTCTTCAAATCCTTAGAAGGAGCTCTCTCGATGCATCGAA...

Protein

Download Protein FASTA

790 aa · LXL04_008651|LXL04_008651|OH1004|PROTEIN

MLHGRRKTTSPNKPLFRYPLIRSKTTIIKPSTSKSKLGTFLVVASIVKSLSEPGGTRNFNNGESSLVSLSEPLVLQILRRSSLDASKKIDFFKWCSLRHNYKQSAGTYSQMLQTLCINPVVHKNDIFDFLASMNREGVVLESSTFKFILDSFIKSGNFDYALEIMDHAENILDKLNPDVYNSVLIALIRSNHLNMALFTFFKLLDSITDNNKTSIDAATCNELLVALKRAGMRAEFRNAFDKVREKKNFPIDVRGYNVCI...

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_008651
TK1151 IDTkA03G349330
OH-1004 IDLXL04_008651
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_008651
LocationChr02:105196522-105198894 (+)
DescriptionSimilar to At4g01570: Pentatricopeptide repeat-containing protein At4g01570
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g01570 Pentatricopeptide repeat-containing protein At4g01570. No verified direct reference in this release
At3g53700 May be involved in female gametophyte development. No verified direct reference in this release
At4g28010 Pentatricopeptide repeat-containing protein At4g28010. No verified direct reference in this release
At3g04760 Pentatricopeptide repeat-containing protein At3g04760, chloroplastic. No verified direct reference in this release
At1g64580 Pentatricopeptide repeat-containing protein At1g64580. 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_008651 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0010239 chloroplast mRNA processing Biological Process
GO:0090617 mitochondrial mRNA 5'-end processing Biological Process
GO:0005737 cytoplasm Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0042644 chloroplast nucleoid Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT3G53700
ath:AT4G01570
ath:AT4G28010
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.

Mitochondrion0.764
Rank 1 · LXL04_008651 · OH-1004
Plastid0.132
Rank 2 · LXL04_008651 · OH-1004
Nucleus0.074
Rank 3 · LXL04_008651 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_008651 · OH-1004
Cell membrane0.012
Rank 5 · LXL04_008651 · 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_N238-333 aa
PF13812.13PPR_3246-298 aa
PF13041.13PPR_2252-292 aa
PF01535.27PPR256-283 aa
PF12854.14PPR_1286-314 aa
PF13812.13PPR_3286-334 aa
PF13041.13PPR_2287-336 aa
PF01535.27PPR291-319 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_008651PF29070.1MSC6_N2383337.6e-2485.2
LXL04_008651PF13812.13PPR_32462983.8e-52174.9
LXL04_008651PF13041.13PPR_22522921.6e-93307.4
LXL04_008651PF01535.27PPR2562831.3e-71232.7
LXL04_008651PF12854.14PPR_12863143.9e-70232.0
LXL04_008651PF13812.13PPR_32863343.8e-52174.9
LXL04_008651PF13041.13PPR_22873361.6e-93307.4
LXL04_008651PF01535.27PPR2913191.3e-71232.7
LXL04_008651PF23276.3TPR_242913841.1e-30107.0
LXL04_008651PF12854.14PPR_13193513.9e-70232.0
LXL04_008651PF01535.27PPR3253551.3e-71232.7
LXL04_008651PF17177.11PPR_long3264807.5e-2071.9
LXL04_008651PF13041.13PPR_23293591.6e-93307.4
LXL04_008651PF13812.13PPR_33454023.8e-52174.9
LXL04_008651PF12854.14PPR_13533863.9e-70232.0
LXL04_008651PF13041.13PPR_23574061.6e-93307.4

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
Q8VZE4Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g0157055.226%Swiss-Protstrong database homology
Q9LFF1Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g53700, chloroplastic23.382%Swiss-Protweak database homology
Q9SUD8Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2801028.598%Swiss-Protweak database homology
Q9SR00Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g04760, chloroplastic25.586%Swiss-Protweak database homology
Q0WKZ3Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g6458029.859%Swiss-Protweak database homology

JBrowse

View in Genome Browser