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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_002676
Reference: OH-1004 Chr: Chr01 Coordinates: 54452579-54454894 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2316 bp · LXL04_002676|LXL04_002676|OH1004|cDNA

ATGAGTGAAAGTTTCTGCACTCCAATAATGATTGCCCGCCAATTGATATTCAAATGCATCCACCCTAAAAGAGTAGCAAACTTCCATTCGTTTCAAGATGGGCACCAACTGTTCGTTCAAATTCCTCAGCCAAACCTCGGCTATCTCCACGACTCCATGCTTGATCTATTGCACCAAAACCGACCATTCCAAGCTCTCGATATTTTCAAGAAACAGATTCGGGAAGTGGGCGTTACTCATGTCGATGAAGTTTCTACTGC...

CDS

Download CDS FASTA

2316 bp · LXL04_002676|LXL04_002676|OH1004|CDS

ATGAGTGAAAGTTTCTGCACTCCAATAATGATTGCCCGCCAATTGATATTCAAATGCATCCACCCTAAAAGAGTAGCAAACTTCCATTCGTTTCAAGATGGGCACCAACTGTTCGTTCAAATTCCTCAGCCAAACCTCGGCTATCTCCACGACTCCATGCTTGATCTATTGCACCAAAACCGACCATTCCAAGCTCTCGATATTTTCAAGAAACAGATTCGGGAAGTGGGCGTTACTCATGTCGATGAAGTTTCTACTGC...

Protein

Download Protein FASTA

771 aa · LXL04_002676|LXL04_002676|OH1004|PROTEIN

MSESFCTPIMIARQLIFKCIHPKRVANFHSFQDGHQLFVQIPQPNLGYLHDSMLDLLHQNRPFQALDIFKKQIREVGVTHVDEVSTALATKACRGDPKLGCQIHGFALTSGLDSFLSVSNSLMHMYSKSGQLDRAMVIFEKLTNPGIVSFNTLLSGTNNSTDALNFACRMNHIGVTFDAVTYTSALAHSADCEEFLFGTQLHSLLLKSGMQSEGFIANALITLYSKWEQIVNAEKVFDEMPQKDLVSWNAMLSGYSQEGS...

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_002676
TK1151 IDTkA01G430880
OH-1004 IDLXL04_002676
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)98.600
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_002676
LocationChr01:54452579-54454894 (-)
DescriptionSimilar to PCMP-E40: Pentatricopeptide repeat-containing protein At4g32430, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g32430 Pentatricopeptide repeat-containing protein At4g32430, mitochondrial. No verified direct reference in this release
At2g27610 Pentatricopeptide repeat-containing protein At2g27610. No verified direct reference in this release
At4g39530 Pentatricopeptide repeat-containing protein At4g39530. No verified direct reference in this release
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
At3g25970 Putative pentatricopeptide repeat-containing protein At3g25970. 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_002676 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:1905639 positive regulation of mitochondrial mRNA catabolic process 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:AT2G27610
ath:AT4G32430
ath:AT4G39530
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.

Mitochondrion0.733
Rank 1 · LXL04_002676 · OH-1004
Plastid0.128
Rank 2 · LXL04_002676 · OH-1004
Nucleus0.051
Rank 3 · LXL04_002676 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_002676 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_002676 · 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_2244-287 aa
PF13041.13PPR_2346-386 aa
PF29070.1MSC6_N363-489 aa
PF13041.13PPR_2443-485 aa
PF29070.1MSC6_N536-636 aa
PF13041.13PPR_2542-589 aa
PF01535.27PPR544-571 aa
PF13812.13PPR_3565-625 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_002676PF13041.13PPR_22442871.3e-52176.4
LXL04_002676PF13041.13PPR_23463861.3e-52176.4
LXL04_002676PF29070.1MSC6_N3634891.3e-1971.3
LXL04_002676PF13041.13PPR_24434851.3e-52176.4
LXL04_002676PF29070.1MSC6_N5366361.3e-1971.3
LXL04_002676PF13041.13PPR_25425891.3e-52176.4
LXL04_002676PF01535.27PPR5445716.8e-51167.7
LXL04_002676PF13812.13PPR_35656251.2e-1764.4
LXL04_002676PF01535.27PPR5796076.8e-51167.7
LXL04_002676PF20431.5E_motif6597217.1e-2071.7

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
Q84MA3Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g32430, mitochondrial49.728%Swiss-Protmoderate database homology
Q9ZUW3Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2761031.714%Swiss-Protmoderate database homology
Q9SVA5Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3953031.878%Swiss-Protmoderate database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic31.304%Swiss-Protmoderate database homology
Q9LU94Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g2597030.963%Swiss-Protmoderate database homology

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