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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_024423
Reference: OH-1004 Chr: Chr05 Coordinates: 90143485-90145617 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2133 bp · LXL04_024423|LXL04_024423|OH1004|cDNA

ATGATCCAAATCTCGTCATACCCTTTACATCACTTCACTCATTTGCTTAAAACATGCATTTCTCATAGAGATCTCTTAACCGGAAAATCTCTCCACGCCCTCTACATCAAAACCGTCATCCCTCCTTCCACTTACCTTTCCAATCACTTCATCCTCCTCTACTCCAAATGTCGGCGTCTCTGCGCCGCCCGCAACGCCTTTGATGGTATCCCACATCCAAATGTCTTCTCCTTCAACACTATTGTCTCCGCCTACGCGAA...

CDS

Download CDS FASTA

2133 bp · LXL04_024423|LXL04_024423|OH1004|CDS

ATGATCCAAATCTCGTCATACCCTTTACATCACTTCACTCATTTGCTTAAAACATGCATTTCTCATAGAGATCTCTTAACCGGAAAATCTCTCCACGCCCTCTACATCAAAACCGTCATCCCTCCTTCCACTTACCTTTCCAATCACTTCATCCTCCTCTACTCCAAATGTCGGCGTCTCTGCGCCGCCCGCAACGCCTTTGATGGTATCCCACATCCAAATGTCTTCTCCTTCAACACTATTGTCTCCGCCTACGCGAA...

Protein

Download Protein FASTA

710 aa · LXL04_024423|LXL04_024423|OH1004|PROTEIN

MIQISSYPLHHFTHLLKTCISHRDLLTGKSLHALYIKTVIPPSTYLSNHFILLYSKCRRLCAARNAFDGIPHPNVFSFNTIVSAYAKESQPLIAHQLFDQIPEPDLVSYNTLISAYADRGDTQPALHLFMEMRELGFDMDGFTFSAAITAACKDIWLIRQLHKLAISGGFNAYTSVNNSLVTYYSKNGYLDDAKSIFDSMGSDKDEVTWNSMIVAHSQHREGLEALELYRKMVYLELPIDTFSFASVLTAFTCLEDLRGG...

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_024423
TK1151 IDTkA06G145470
OH-1004 IDLXL04_024423
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)80.400
Protein coverage (%)TK1151 100.000 / OH-1004 71.972
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_024423
LocationChr05:90143485-90145617 (-)
DescriptionSimilar to PCMP-H79: Pentatricopeptide repeat-containing protein At3g49710
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g49710 Pentatricopeptide repeat-containing protein At3g49710. No verified direct reference in this release
At2g22070 Pentatricopeptide repeat-containing protein At2g22070. 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
At3g02010 Putative pentatricopeptide repeat-containing protein At2g01510. No verified direct reference in this release
At1g68930 Putative pentatricopeptide repeat-containing protein At1g68930. 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_024423 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016556 mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0004519 endonuclease activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G11290
ath:AT2G22070
ath:AT3G02010
ath:AT3G49710
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.

Mitochondrion0.641
Rank 1 · LXL04_024423 · OH-1004
Plastid0.204
Rank 2 · LXL04_024423 · OH-1004
Nucleus0.058
Rank 3 · LXL04_024423 · OH-1004
Cytoplasm0.038
Rank 4 · LXL04_024423 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_024423 · 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.

PF12854.14PPR_1103-133 aa
PF13812.13PPR_3103-138 aa
PF13041.13PPR_2104-153 aa
PF01535.27PPR107-137 aa
PF13041.13PPR_2205-251 aa
PF01535.27PPR207-233 aa
PF13041.13PPR_2306-353 aa
PF01535.27PPR383-410 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_024423PF12854.14PPR_11031336.9e-43144.8
LXL04_024423PF13812.13PPR_31031389.2e-2896.8
LXL04_024423PF13041.13PPR_21041531.9e-69230.3
LXL04_024423PF01535.27PPR1071374.6e-61199.6
LXL04_024423PF13041.13PPR_22052511.9e-69230.3
LXL04_024423PF01535.27PPR2072334.6e-61199.6
LXL04_024423PF13041.13PPR_23063531.9e-69230.3
LXL04_024423PF01535.27PPR3834104.6e-61199.6
LXL04_024423PF13812.13PPR_34094569.2e-2896.8
LXL04_024423PF13041.13PPR_24104581.9e-69230.3
LXL04_024423PF29070.1MSC6_N4115063.2e-1350.3
LXL04_024423PF13812.13PPR_34334939.2e-2896.8
LXL04_024423PF12854.14PPR_14775086.9e-43144.8
LXL04_024423PF01535.27PPR4845094.6e-61199.6
LXL04_024423PF20431.5E_motif5275894.6e-2072.3
LXL04_024423PF14432.13DYW_deaminase6327104.7e-30104.0

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
Q9M2Y7Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g4971060.028%Swiss-Protstrong database homology
Q9SHZ8Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2207036.788%Swiss-Protmoderate database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic36.428%Swiss-Protmoderate database homology
Q9S7F4Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At2g0151037.481%Swiss-Protmoderate database homology
Q9CAA8Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At1g6893034.951%Swiss-Protmoderate database homology

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