LXL04_000746 | RubberDandelionOmics

Gene overview

LXL04_000746

Reference: OH-1004 Chr: Chr01 Coordinates: 13788733-13789525 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

734 bp · LXL04_000746|LXL04_000746|OH1004|cDNA

CAATTAGGCATTCTGCTATGCTGAATTACACACGAACCATTCTTAGAAGAACTTCATTGTCCAATCTCATTTATTTCAATCACACGCATACAATCTCAACCTTGTCATCAAGCCCTAGCTTATCAATATGGAGACGAAAGAAGGAATTGGGAAAAGAAGGTTTAATAATTACAAAAGAGCTCAAGAGACTTCAATCCAGTCCTCCCAGACTTGACCGATTCATCAAATCCCATGTCTCTCGCCTTCTCAAATCCGACCTT...

CDS

Download CDS FASTA

717 bp · LXL04_000746|LXL04_000746|OH1004|CDS

ATGCTGAATTACACACGAACCATTCTTAGAAGAACTTCATTGTCCAATCTCATTTATTTCAATCACACGCATACAATCTCAACCTTGTCATCAAGCCCTAGCTTATCAATATGGAGACGAAAGAAGGAATTGGGAAAAGAAGGTTTAATAATTACAAAAGAGCTCAAGAGACTTCAATCCAGTCCTCCCAGACTTGACCGATTCATCAAATCCCATGTCTCTCGCCTTCTCAAATCCGACCTTGTTTCTGTTCTTTTTGA...

Protein

Download Protein FASTA

238 aa · LXL04_000746|LXL04_000746|OH1004|PROTEIN

MLNYTRTILRRTSLSNLIYFNHTHTISTLSSSPSLSIWRRKKELGKEGLIITKELKRLQSSPPRLDRFIKSHVSRLLKSDLVSVLFEFQRQDLVFLSMKLYEVVRKEIWYRPDMFFYRDMLMMLARNKKAEEIKRVWDDLTKEEVHFDQHTFGDIIRAFLDSGLALEAMFVYDEMRKSPDPPLSLPYRVILKGLLVYPELREKVKDDFLELFPGMVIYDPPEGLFEECLSSEEGVESN

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.

ID Mapping

Input ID	`LXL04_000746`
TK1151 ID	TkA01G590420
OH-1004 ID	LXL04_000746
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.900
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 version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_000746

Location Chr01:13788733-13789525 (+)

Description Similar to At1g62350: Pentatricopeptide repeat-containing protein At1g62350

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g62350`	Pentatricopeptide repeat-containing protein At1g62350.	No verified direct reference in this release
`At3g46870`	Binds weakly to specific single strand RNA (ssRNA).	Structure of a PLS-class pentatricopeptide repeat protein provides insights into mechanism of RNA recognition.2013 · DOI: 10.1074/jbc.m113.496828
`At3g27750`	Essential protein required during embryogenesis.	A short PPR protein required for the splicing of specific group II introns in angiosperm chloroplasts.2012 · DOI: 10.1261/rna.032623.112 Structure of a PLS-class pentatricopeptide repeat protein provides insights into mechanism of RNA recognition.2013 · DOI: 10.1074/jbc.m113.496828
`At1g74850`	Involved in plastid gene expression.	pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression.2006 · DOI: 10.1105/tpc.105.036392
`At1g62910`	Pentatricopeptide repeat-containing protein At1g62910.	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_000746 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000373 Group II intron splicing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0042793 plastid transcription Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0090617 mitochondrial mRNA 5'-end processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0042644 chloroplast nucleoid Cellular Component

KEGG gene cross-reference

ath:AT1G62350

ath:AT1G62910

ath:AT1G74850

ath:AT3G27750

ath:AT3G46870

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Mitochondrion0.843

Rank 1 · LXL04_000746 · OH-1004

Plastid0.097

Rank 2 · LXL04_000746 · OH-1004

Nucleus0.049

Rank 3 · LXL04_000746 · OH-1004

Cytoplasm0.036

Rank 4 · LXL04_000746 · OH-1004

Cell membrane0.011

Rank 5 · LXL04_000746 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

No result was found for this query.

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

Protein	Organism	Description	Identity	Database	Confidence
`Q1PFH7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62350	76.440%	Swiss-Prot	strong database homology
`Q9STF9`	Arabidopsis thaliana	Protein THYLAKOID ASSEMBLY 8-like, chloroplastic	43.882%	Swiss-Prot	moderate database homology
`Q9LVW6`	Arabidopsis thaliana	Protein THYLAKOID ASSEMBLY 8, chloroplastic	29.310%	Swiss-Prot	weak database homology
`Q9S7Q2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g74850, chloroplastic	22.892%	Swiss-Prot	weak database homology
`Q9LQ16`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62910	28.244%	Swiss-Prot	weak database homology

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