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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_001890
Reference: OH-1004 Chr: Chr01 Coordinates: 36291424-36293568 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2145 bp · LXL04_001890|LXL04_001890|OH1004|cDNA

ATGTTAGCAAAACGAAATTACATCCATATTCACGATTTGATTATTCGTAATGTGGTTAGATTTAATCACTCACCTTCCTTATCATCAATTCCCTTAAACCCTAATTATCGTCCAAGCAAATCCATCATCCATTGCAACTCCAAGATCAGCGAAAATGGTCGAAATGGTAAAATCAACGAGGCAGAATATATATTCTATCACATGCCGGTCAAGACTGTGGTATCATGGACTGCTATGCTCACCGCATACGCAGATAACGG...

CDS

Download CDS FASTA

2145 bp · LXL04_001890|LXL04_001890|OH1004|CDS

ATGTTAGCAAAACGAAATTACATCCATATTCACGATTTGATTATTCGTAATGTGGTTAGATTTAATCACTCACCTTCCTTATCATCAATTCCCTTAAACCCTAATTATCGTCCAAGCAAATCCATCATCCATTGCAACTCCAAGATCAGCGAAAATGGTCGAAATGGTAAAATCAACGAGGCAGAATATATATTCTATCACATGCCGGTCAAGACTGTGGTATCATGGACTGCTATGCTCACCGCATACGCAGATAACGG...

Protein

Download Protein FASTA

714 aa · LXL04_001890|LXL04_001890|OH1004|PROTEIN

MLAKRNYIHIHDLIIRNVVRFNHSPSLSSIPLNPNYRPSKSIIHCNSKISENGRNGKINEAEYIFYHMPVKTVVSWTAMLTAYADNGQIHNARKLFDEMPQRNIATWNAMITAYTRNRNGIDKACDLFSKSPEKNAVSYASMITGYVRAGRLDDALKLYNSTPLKWRDPFCSNALMNGYLKNGKLKEAVLIYNKMVERNVVSWTSMIDGCCKLGEIKKARELFNAIPERNVFTWTAMIDGYMKSIYFEDGFSLFLQMRHE...

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_001890
TK1151 IDTkA01G500620
OH-1004 IDLXL04_001890
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)98.400
Protein coverage (%)TK1151 84.351 / OH-1004 61.905
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_001890
LocationChr01:36291424-36293568 (-)
DescriptionSimilar to PCMP-E63: Pentatricopeptide repeat-containing protein At1g53600, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g53600 Pentatricopeptide repeat-containing protein At1g53600, mitochondrial. No verified direct reference in this release
At1g32415 Pentatricopeptide repeat-containing protein At1g32415, mitochondrial. No verified direct reference in this release
At4g02750 Pentatricopeptide repeat-containing protein At4g02750. No verified direct reference in this release
At1g09410 Pentatricopeptide repeat-containing protein At1g09410, mitochondrial. No verified direct reference in this release
At1g56690 Pentatricopeptide repeat-containing protein At1g56690, 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_001890 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0010214 seed coat development Biological Process
GO:0031930 mitochondria-nucleus signaling pathway Biological Process
GO:0140547 acquisition of seed longevity Biological Process
GO:1905392 plant organ morphogenesis Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G32415
ath:AT1G53600
ath:AT4G02750
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.

Mitochondrion0.672
Rank 1 · LXL04_001890 · OH-1004
Plastid0.153
Rank 2 · LXL04_001890 · OH-1004
Nucleus0.050
Rank 3 · LXL04_001890 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_001890 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_001890 · 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.

PF13041.13PPR_272-104 aa
PF01535.27PPR74-104 aa
PF13041.13PPR_2134-160 aa
PF12854.14PPR_1135-160 aa
PF01535.27PPR137-160 aa
PF13041.13PPR_2170-200 aa
PF01535.27PPR173-200 aa
PF12854.14PPR_1195-224 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_001890PF13041.13PPR_2721041.6e-90297.8
LXL04_001890PF01535.27PPR741044.6e-93299.9
LXL04_001890PF13041.13PPR_21341601.6e-90297.8
LXL04_001890PF12854.14PPR_11351604.3e-66219.0
LXL04_001890PF01535.27PPR1371604.6e-93299.9
LXL04_001890PF13041.13PPR_21702001.6e-90297.8
LXL04_001890PF01535.27PPR1732004.6e-93299.9
LXL04_001890PF12854.14PPR_11952244.3e-66219.0
LXL04_001890PF13041.13PPR_21982311.6e-90297.8
LXL04_001890PF01535.27PPR2012304.6e-93299.9
LXL04_001890PF13041.13PPR_22292771.6e-90297.8
LXL04_001890PF01535.27PPR2322604.6e-93299.9
LXL04_001890PF01535.27PPR3653914.6e-93299.9
LXL04_001890PF13041.13PPR_23944381.6e-90297.8
LXL04_001890PF29070.1MSC6_N3954832.9e-1763.6
LXL04_001890PF01535.27PPR3964224.6e-93299.9

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
Q9C8L6Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g53600, mitochondrial49.081%Swiss-Protmoderate database homology
P0C7R0Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g32415, mitochondrial37.090%Swiss-Protmoderate database homology
Q9SY02Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g0275035.933%Swiss-Protmoderate database homology
Q56XI1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g09410, mitochondrial33.603%Swiss-Protmoderate database homology
Q9FXB9Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g56690, mitochondrial32.504%Swiss-Protmoderate database homology

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