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_038833
Reference: OH-1004 Chr: Chr09 Coordinates: 51626551-51628890 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2115 bp · LXL04_038833|LXL04_038833|OH1004|cDNA

ATGACGCTAGCTCGATTACTCATCCGCTCCCTCTGCCGTCCCTCATCTCTCCGGGCCACCGCTACCACGGCTGCTTCCTTCAACATCCAATCTCCATCTCTCCCATCTCAAACAGCAAACCCTAACTTCCTTATCCCTGTTAGATCCTTCGCCTTTTCTTCAGCCGAGGAAGCTGCGGCCGAACGCCGACGTCGCAAACGTCGCCTCCGTATCGAGCCCCCGTTACACGCCCTCCAGCGTGATCCCAATGCCCCACGGCC...

CDS

Download CDS FASTA

2115 bp · LXL04_038833|LXL04_038833|OH1004|CDS

ATGACGCTAGCTCGATTACTCATCCGCTCCCTCTGCCGTCCCTCATCTCTCCGGGCCACCGCTACCACGGCTGCTTCCTTCAACATCCAATCTCCATCTCTCCCATCTCAAACAGCAAACCCTAACTTCCTTATCCCTGTTAGATCCTTCGCCTTTTCTTCAGCCGAGGAAGCTGCGGCCGAACGCCGACGTCGCAAACGTCGCCTCCGTATCGAGCCCCCGTTACACGCCCTCCAGCGTGATCCCAATGCCCCACGGCC...

Protein

Download Protein FASTA

704 aa · LXL04_038833|LXL04_038833|OH1004|PROTEIN

MTLARLLIRSLCRPSSLRATATTAASFNIQSPSLPSQTANPNFLIPVRSFAFSSAEEAAAERRRRKRRLRIEPPLHALQRDPNAPRPRRDPNQPDTTSALVGPRLSLHNRVQSLIRAGDLDNASVVARQSVFSSTRPTVFTCNAIIGSMYRAKRYLDAIALFAYFFKQCNIVPNVVSYNFLIVSHCENGEVDKALEVYQHIKDNAPFSPSAVTFRHLTKGLIDAGRINEAVEMLWKMVGDGHGADSQVFNNIISGFLNLN...

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_038833
TK1151 IDTkA04G469890
OH-1004 IDLXL04_038833
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.000
Protein coverage (%)TK1151 84.211 / OH-1004 84.091
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_038833
LocationChr09:51626551-51628890 (+)
DescriptionSimilar to GRP23: Pentatricopeptide repeat-containing protein At1g10270
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g10270 May function as a transcriptional regulator essential for early embryogenesis.
Arabidopsis GLUTAMINE-RICH PROTEIN23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNA polymerase II subunit III.2006 · DOI: 10.1105/tpc.105.039495
At3g49240 May play a role in embryogenesis. No verified direct reference in this release
At3g60980 Pentatricopeptide repeat-containing protein At3g60980, mitochondrial. No verified direct reference in this release
At3g60960 Pentatricopeptide repeat-containing protein At3g60960, mitochondrial. No verified direct reference in this release
At1g09900 Pentatricopeptide repeat-containing protein At1g09900. 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_038833 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006351 DNA-templated transcription Biological Process
GO:0006979 response to oxidative stress Biological Process
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0009960 endosperm development Biological Process
GO:0051301 cell division Biological Process
GO:0005634 nucleus Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003729 mRNA binding Molecular Function
GO:0005524 ATP binding Molecular Function
KEGG gene cross-reference
ath:AT1G09900
ath:AT1G10270
ath:AT3G49240
ath:AT3G60960
ath:AT3G60980
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.

Mitochondrion0.696
Rank 1 · LXL04_038833 · OH-1004
Plastid0.258
Rank 2 · LXL04_038833 · OH-1004
Nucleus0.056
Rank 3 · LXL04_038833 · OH-1004
Cytoplasm0.040
Rank 4 · LXL04_038833 · OH-1004
Cell membrane0.016
Rank 5 · LXL04_038833 · 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_N142-269 aa
PF12854.14PPR_1170-198 aa
PF13041.13PPR_2173-221 aa
PF01535.27PPR176-203 aa
PF23276.3TPR_24176-270 aa
PF29070.1MSC6_N285-379 aa
PF29070.1MSC6_N355-517 aa
PF13041.13PPR_2394-439 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_038833PF29070.1MSC6_N1422692.9e-1970.2
LXL04_038833PF12854.14PPR_11701984.7e-37126.1
LXL04_038833PF13041.13PPR_21732211.7e-50169.6
LXL04_038833PF01535.27PPR1762037.3e-40133.2
LXL04_038833PF23276.3TPR_241762701.2e-1661.5
LXL04_038833PF29070.1MSC6_N2853792.9e-1970.2
LXL04_038833PF29070.1MSC6_N3555172.9e-1970.2
LXL04_038833PF13041.13PPR_23944391.7e-50169.6
LXL04_038833PF12854.14PPR_14254574.7e-37126.1
LXL04_038833PF13041.13PPR_24284611.7e-50169.6
LXL04_038833PF23276.3TPR_244315251.2e-1661.5
LXL04_038833PF01535.27PPR4324617.3e-40133.2
LXL04_038833PF13041.13PPR_24745111.7e-50169.6

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
Q9SY69Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1027061.240%Swiss-Protstrong database homology
Q9M3A8Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g49240, mitochondrial36.023%Swiss-Protmoderate database homology
Q9LEX5Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g60980, mitochondrial38.421%Swiss-Protmoderate database homology
Q9LEX6Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g60960, mitochondrial33.659%Swiss-Protmoderate database homology
Q3EDF8Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g0990022.360%Swiss-Protweak database homology

JBrowse

View in Genome Browser