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_016679
Reference: OH-1004 Chr: Chr03 Coordinates: 130709506-130710651 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1146 bp · LXL04_016679|LXL04_016679|OH1004|cDNA

ATGATTTCTCGTCCGATCGTAGCTTGCAATACCAAACTTCCCAAAACCTATCTGATCTTCCTTCAACTAAACTTGTATCACTCAACTGTTTCACTCAGTTCTTCTATAAAACTCGATCCCCTCGACTTACGCAATTACAAAGACTGGTTAAGTCCGACTGAAGTCATCAAGATTTTCGAAACCCTAAAAAATCCCAATTCGACCCTTACAGTTCTCAATCAGCTCTCGAAGCGGAAAGATTATAAACCCAATGAAGCTCT...

CDS

Download CDS FASTA

1146 bp · LXL04_016679|LXL04_016679|OH1004|CDS

ATGATTTCTCGTCCGATCGTAGCTTGCAATACCAAACTTCCCAAAACCTATCTGATCTTCCTTCAACTAAACTTGTATCACTCAACTGTTTCACTCAGTTCTTCTATAAAACTCGATCCCCTCGACTTACGCAATTACAAAGACTGGTTAAGTCCGACTGAAGTCATCAAGATTTTCGAAACCCTAAAAAATCCCAATTCGACCCTTACAGTTCTCAATCAGCTCTCGAAGCGGAAAGATTATAAACCCAATGAAGCTCT...

Protein

Download Protein FASTA

381 aa · LXL04_016679|LXL04_016679|OH1004|PROTEIN

MISRPIVACNTKLPKTYLIFLQLNLYHSTVSLSSSIKLDPLDLRNYKDWLSPTEVIKIFETLKNPNSTLTVLNQLSKRKDYKPNEALYTSVINNLSEAKNFDGIEEVMKRIKVEKSCRLSDGFFYNVIRIYGLRAGRINRAIETLFDMPNYSSWPTPKTFNFVLNLLVNTKQFDVIHEVYMGAGKLGVEVDACCLNIMIKGLCKNGKINDALQVFDEFPKQNCKPNVRTFSTLMHGLCSLGRVEEAFSLLQKMETEGIEP...

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_016679
TK1151 IDTkA02G112170
OH-1004 IDLXL04_016679
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.500
Protein coverage (%)TK1151 95.012 / 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_016679
LocationChr03:130709506-130710651 (+)
DescriptionSimilar to At3g14580: Pentatricopeptide repeat-containing protein At3g14580, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g14580 Pentatricopeptide repeat-containing protein At3g14580, mitochondrial. No verified direct reference in this release
At5g46100 Pentatricopeptide repeat-containing protein At5g46100. No verified direct reference in this release
At4g20090 May play a role in embryogenesis. No verified direct reference in this release
At1g74580 Putative pentatricopeptide repeat-containing protein At1g74580. No verified direct reference in this release
At5g16420 Pentatricopeptide repeat-containing protein At5g16420, mitochondrial. 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_016679 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT3G14580
ath:AT4G20090
ath:AT5G46100
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.

Mitochondrion0.864
Rank 1 · LXL04_016679 · OH-1004
Plastid0.064
Rank 2 · LXL04_016679 · OH-1004
Nucleus0.048
Rank 3 · LXL04_016679 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_016679 · OH-1004
Cell membrane0.011
Rank 5 · LXL04_016679 · 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.

PF23276.3TPR_24116-217 aa
PF17177.11PPR_long157-288 aa
PF13041.13PPR_2158-204 aa
PF13812.13PPR_3185-234 aa
PF12854.14PPR_1187-217 aa
PF29070.1MSC6_N190-282 aa
PF13041.13PPR_2191-238 aa
PF01535.27PPR195-223 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_016679PF23276.3TPR_241162173.1e-1453.7
LXL04_016679PF17177.11PPR_long1572888.8e-1555.4
LXL04_016679PF13041.13PPR_21582041.8e-44150.3
LXL04_016679PF13812.13PPR_31852342.1e-1970.1
LXL04_016679PF12854.14PPR_11872174.6e-40135.8
LXL04_016679PF29070.1MSC6_N1902822.4e-1660.5
LXL04_016679PF13041.13PPR_21912381.8e-44150.3
LXL04_016679PF01535.27PPR1952231.7e-33113.2
LXL04_016679PF12854.14PPR_12222544.6e-40135.8
LXL04_016679PF01535.27PPR2292581.7e-33113.2
LXL04_016679PF23276.3TPR_242293193.1e-1453.7
LXL04_016679PF13041.13PPR_22322731.8e-44150.3
LXL04_016679PF13812.13PPR_32483042.1e-1970.1
LXL04_016679PF12854.14PPR_12572884.6e-40135.8
LXL04_016679PF13041.13PPR_22643011.8e-44150.3
LXL04_016679PF01535.27PPR2662931.7e-33113.2

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
Q9LUD6Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g14580, mitochondrial56.851%Swiss-Protstrong database homology
Q9FNL2Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g4610026.488%Swiss-Protweak database homology
O49436Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2009030.137%Swiss-Protmoderate database homology
Q9CA58Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At1g7458024.377%Swiss-Protweak database homology
Q9FFE3Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g16420, mitochondrial25.672%Swiss-Protweak database homology

JBrowse

View in Genome Browser