LXL04_026085 | RubberDandelionOmics

Gene overview

LXL04_026085

Reference: OH-1004 Chr: Chr05 Coordinates: 120720899-120723388 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2490 bp · LXL04_026085|LXL04_026085|OH1004|cDNA

ATGTACCAAAAGAACCTCTTTTTATTTCACAGGAGATTTTCCCaaatatcatcatcatcatcaataAGCACAAACACGTTTATTGAGAATTTCCCCAATACCAAGGAAGTTTTAATATCCAAACTTGCATCAGTCTTGCAATCATGTTCAACCCCTAATCCTGATCCTCGAGTCGTCCAACAAGGCCAACAACTTCATGCCCAGATAATCGTCAATGGGATCAACCATATCGGCCTTTTGGGTTCAAGATTACTCGGAAT...

CDS

Download CDS FASTA

2490 bp · LXL04_026085|LXL04_026085|OH1004|CDS

ATGTACCAAAAGAACCTCTTTTTATTTCACAGGAGATTTTCCCAAATATCATCATCATCATCAATAAGCACAAACACGTTTATTGAGAATTTCCCCAATACCAAGGAAGTTTTAATATCCAAACTTGCATCAGTCTTGCAATCATGTTCAACCCCTAATCCTGATCCTCGAGTCGTCCAACAAGGCCAACAACTTCATGCCCAGATAATCGTCAATGGGATCAACCATATCGGCCTTTTGGGTTCAAGATTACTCGGAAT...

Protein

Download Protein FASTA

829 aa · LXL04_026085|LXL04_026085|OH1004|PROTEIN

MYQKNLFLFHRRFSQISSSSSISTNTFIENFPNTKEVLISKLASVLQSCSTPNPDPRVVQQGQQLHAQIIVNGINHIGLLGSRLLGMYILCKKLDDANTIFRQLDLFYASPWNWMIRGFTMMGCFNYAVMVYFKMLGYGTCPDKYTFPYVIKACGQLGGIRLVKSIHQTIQTMGFETDVYVGSSLIKLYAENGCIDNARHLFDKMPQRDDVLWNVILNGYLKHGDPKHVLSLFNQMRSSITQPGSVTYACVLSACDANIK...

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_026085`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_026085

Location Chr05:120720899-120723388 (-)

Description Similar to PCMP-E36: Pentatricopeptide repeat-containing protein At4g21300

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21300`	Pentatricopeptide repeat-containing protein At4g21300.	No verified direct reference in this release
`At3g03580`	Pentatricopeptide repeat-containing protein At3g03580.	No verified direct reference in this release
`At3g63370`	Involved in RNA editing event in chloroplasts.	A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
`At4g13650`	Pentatricopeptide repeat-containing protein At4g13650.	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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026085 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT3G03580

ath:AT4G21300

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.

Mitochondrion0.647

Rank 1 · LXL04_026085 · OH-1004

Plastid0.203

Rank 2 · LXL04_026085 · OH-1004

Nucleus0.048

Rank 3 · LXL04_026085 · OH-1004

Cytoplasm0.033

Rank 4 · LXL04_026085 · OH-1004

Cell membrane0.006

Rank 5 · LXL04_026085 · 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_2112-154 aa

PF13041.13PPR_2209-255 aa

PF01535.27PPR211-238 aa

PF12854.14PPR_1306-335 aa

PF13041.13PPR_2307-348 aa

PF01535.27PPR310-338 aa

PF13041.13PPR_2409-456 aa

PF01535.27PPR483-508 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026085	`PF13041.13`	PPR_2	112	154	1.2e-83	275.7
LXL04_026085	`PF13041.13`	PPR_2	209	255	1.2e-83	275.7
LXL04_026085	`PF01535.27`	PPR	211	238	5.6e-80	258.9
LXL04_026085	`PF12854.14`	PPR_1	306	335	3.5e-51	171.3
LXL04_026085	`PF13041.13`	PPR_2	307	348	1.2e-83	275.7
LXL04_026085	`PF01535.27`	PPR	310	338	5.6e-80	258.9
LXL04_026085	`PF13041.13`	PPR_2	409	456	1.2e-83	275.7
LXL04_026085	`PF01535.27`	PPR	483	508	5.6e-80	258.9
LXL04_026085	`PF13041.13`	PPR_2	508	554	1.2e-83	275.7
LXL04_026085	`PF12854.14`	PPR_1	508	536	3.5e-51	171.3
LXL04_026085	`PF01535.27`	PPR	511	537	5.6e-80	258.9
LXL04_026085	`PF13041.13`	PPR_2	607	653	1.2e-83	275.7
LXL04_026085	`PF01535.27`	PPR	609	638	5.6e-80	258.9
LXL04_026085	`PF20431.5`	E_motif	724	786	5.6e-21	75.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9STE1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g21300	50.936%	Swiss-Prot	strong database homology
`Q9SS60`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g03580	36.340%	Swiss-Prot	moderate database homology
`Q9M1V3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g63370, chloroplastic	35.975%	Swiss-Prot	moderate database homology
`Q9SVP7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g13650	34.300%	Swiss-Prot	moderate database homology
`Q3E6Q1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g11290, chloroplastic	36.711%	Swiss-Prot	moderate database homology

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