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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_003612
Reference: OH-1004 Chr: Chr01 Coordinates: 88897228-88898887 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1485 bp · LXL04_003612|LXL04_003612|OH1004|cDNA

ATGTCGTCGTTGGCACCGCCGTCATCGTCTCTCTCGTTCTCATCCTCCCTATCATTGTCCTCCAACAGTTACCGAAATCTCCACCACCGTCACCGCATTCACTATCCCATAACATCTCCTCGGTTCCTATTTCGATGTGCAATGAGGTCAGCTTCATCAGTTGCTGCACCAAAGAAGAAGAAGCTATGGAAGCAAGGGGAGTACCCCGGCGATGTGGCGGGGACTTCGAGTTTCGACAGGAACAAGAGAAGAACACCGAA...

CDS

Download CDS FASTA

1485 bp · LXL04_003612|LXL04_003612|OH1004|CDS

ATGTCGTCGTTGGCACCGCCGTCATCGTCTCTCTCGTTCTCATCCTCCCTATCATTGTCCTCCAACAGTTACCGAAATCTCCACCACCGTCACCGCATTCACTATCCCATAACATCTCCTCGGTTCCTATTTCGATGTGCAATGAGGTCAGCTTCATCAGTTGCTGCACCAAAGAAGAAGAAGCTATGGAAGCAAGGGGAGTACCCCGGCGATGTGGCGGGGACTTCGAGTTTCGACAGGAACAAGAGAAGAACACCGAA...

Protein

Download Protein FASTA

494 aa · LXL04_003612|LXL04_003612|OH1004|PROTEIN

MSSLAPPSSSLSFSSSLSLSSNSYRNLHHRHRIHYPITSPRFLFRCAMRSASSVAAPKKKKLWKQGEYPGDVAGTSSFDRNKRRTPNKNIKKKADRKDNLNSWVNTVTEAFTESINNKQWLRALEVFEMLKEQPFYQPKHGTYMKLIVLLGKSGQPQHAQNQFNTMIQEGLDPTPELYTALLAAYTRNNLLDPAFNILNQMNNHPSIQPDIHTYSILIKACVDASRFDLVQSLYEEMTKIPLTPNTLTQNTVLAGYGKAG...

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.

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ID Mapping

Input IDLXL04_003612
TK1151 IDTkA01G324550
OH-1004 IDLXL04_003612
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)97.000
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_003612
LocationChr01:88897228-88898887 (-)
DescriptionSimilar to EMB2750: Pentatricopeptide repeat-containing protein At3g06430, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g06430 Pentatricopeptide repeat-containing protein At3g06430, chloroplastic. No verified direct reference in this release
At5g48730 Pentatricopeptide repeat-containing protein At5g48730, chloroplastic. No verified direct reference in this release
At3g53170 Pentatricopeptide repeat-containing protein At3g53170. No verified direct reference in this release
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release
At4g39620 Essential for embryo development. 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_003612 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009553 embryo sac development Biological Process
GO:0009555 pollen development Biological Process
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0048868 pollen tube development Biological Process
GO:0005730 nucleolus Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003729 mRNA binding Molecular Function
GO:0019843 rRNA binding Molecular Function
KEGG gene cross-reference
ath:AT3G06430
ath:AT3G53170
ath:AT5G02860
ath:AT5G48730
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.

Plastid0.789
Rank 1 · LXL04_003612 · OH-1004
Mitochondrion0.156
Rank 2 · LXL04_003612 · OH-1004
Nucleus0.041
Rank 3 · LXL04_003612 · OH-1004
Cytoplasm0.017
Rank 4 · LXL04_003612 · OH-1004
Cell membrane0.009
Rank 5 · LXL04_003612 · 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.

PF17177.11PPR_long120-237 aa
PF29070.1MSC6_N142-236 aa
PF23276.3TPR_24142-242 aa
PF13812.13PPR_3177-223 aa
PF13041.13PPR_2178-222 aa
PF13812.13PPR_3197-258 aa
PF29070.1MSC6_N238-340 aa
PF13812.13PPR_3277-327 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_003612PF17177.11PPR_long1202375.1e-1762.7
LXL04_003612PF29070.1MSC6_N1422364.6e-2382.7
LXL04_003612PF23276.3TPR_241422425.6e-1659.4
LXL04_003612PF13812.13PPR_31772232.6e-29101.8
LXL04_003612PF13041.13PPR_21782222.9e-50168.9
LXL04_003612PF13812.13PPR_31972582.6e-29101.8
LXL04_003612PF29070.1MSC6_N2383404.6e-2382.7
LXL04_003612PF13812.13PPR_32773272.6e-29101.8
LXL04_003612PF13041.13PPR_22803292.9e-50168.9
LXL04_003612PF23276.3TPR_243364475.6e-1659.4
LXL04_003612PF13041.13PPR_23523992.9e-50168.9
LXL04_003612PF13812.13PPR_34184672.6e-29101.8
LXL04_003612PF13041.13PPR_24214672.9e-50168.9
LXL04_003612PF01535.27PPR4254531.9e-42141.3

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
Q9SQU6Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g06430, chloroplastic64.877%Swiss-Protstrong database homology
Q9FKC3Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g48730, chloroplastic42.317%Swiss-Protmoderate database homology
Q9SCP4Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g5317037.975%Swiss-Protmoderate database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286031.081%Swiss-Protmoderate database homology
Q9SV96Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g39620, chloroplastic28.280%Swiss-Protweak database homology

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