LXL04_002842 | RubberDandelionOmics

Gene overview

LXL04_002842

Reference: OH-1004 Chr: Chr01 Coordinates: 59424987-59430005 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3040 bp · LXL04_002842|LXL04_002842|OH1004|cDNA

AGGTTTTAGGCAGGGTTTACTCATCGTCTTCTTCAACCTCATTTCCACTCCTTATCCACCCACTTCACCTCTTAAACCAGAAGCCACCATGGCTTCGTCAGCTATTTTCTCCCCAAGCCCTAGAGGCGACCTTCAATCTCCATGGTCAACTAAAAGTATCAAACCAAGAAAACCACAAAAACCCACCACTCATCTCCCCACCCTTCAACTCTTCAAAAACCCGTCTCTAAACCCATTAATTTATTCATCCGCTTTCCCTC...

CDS

Download CDS FASTA

2952 bp · LXL04_002842|LXL04_002842|OH1004|CDS

ATGGCTTCGTCAGCTATTTTCTCCCCAAGCCCTAGAGGCGACCTTCAATCTCCATGGTCAACTAAAAGTATCAAACCAAGAAAACCACAAAAACCCACCACTCATCTCCCCACCCTTCAACTCTTCAAAAACCCGTCTCTAAACCCATTAATTTATTCATCCGCTTTCCCTCACAACCTCAAATTACCATCTCTAAAAGACCCAATTTCATCTACCCATTCTCACCCACTACCAGACTCCGCCGACGAAAATTTCACCAA...

Protein

Download Protein FASTA

983 aa · LXL04_002842|LXL04_002842|OH1004|PROTEIN

MASSAIFSPSPRGDLQSPWSTKSIKPRKPQKPTTHLPTLQLFKNPSLNPLIYSSAFPHNLKLPSLKDPISSTHSHPLPDSADENFTKNLENLATLQRITHGFESVSSPEMNLKRVYIQEPPWITSLLMKNFYRSNVKKRVRFEIDRRNYYILRRRQIKAETEAWEKMTEEYREFQREMCEKKLAPNLPYVKSLFAGWFEPLTKAIEKEQKSPNTKKHQEAYAPYIDSLPADKMAIIVMHKMMGLLMMGHEYRYVRVVQAA...

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_002842`
TK1151 ID	TkA01G417330
OH-1004 ID	LXL04_002842
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.600
Protein coverage (%)	TK1151 99.802 / OH-1004 51.373 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_002842

Location Chr01:59424987-59430005 (+)

Description Similar to RPOT3: DNA-directed RNA polymerase 3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g24120`	Nuclear-encoded DNA-dependent RNA polymerase that catalyzes the transcription of DNA into RNA in chloroplasts using the four ribonucleoside triphosphates as substrates (Probable).	The SCABRA3 nuclear gene encodes the plastid RpoTp RNA polymerase, which is required for chloroplast biogenesis and mesophyll cell proliferation in Arabidopsis.2006 · DOI: 10.1104/pp.106.080069

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002842 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006390 mitochondrial transcription Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

GO:0034245 mitochondrial DNA-directed RNA polymerase complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003899 DNA-directed RNA polymerase activity Molecular Function

KEGG gene cross-reference

ath:AT2G24120

nsy:104216269

nsy:104225149

nta:107783504

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.

Plastid0.566

Rank 1 · LXL04_002842 · OH-1004

Mitochondrion0.459

Rank 2 · LXL04_002842 · OH-1004

Cytoplasm0.055

Rank 3 · LXL04_002842 · OH-1004

Nucleus0.046

Rank 4 · LXL04_002842 · OH-1004

Peroxisome0.012

Rank 5 · LXL04_002842 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF14700.12RPOL_N155-470 aa

PF00940.25RNA_pol592-957 aa

PF00940.25RNA_pol959-983 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002842	`PF14700.12`	RPOL_N	155	470	1.3e-77	262.2
LXL04_002842	`PF00940.25`	RNA_pol	592	957	4.9e-164	547.1
LXL04_002842	`PF00940.25`	RNA_pol	959	983	4.9e-164	547.1

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
`O24600`	Arabidopsis thaliana	DNA-directed RNA polymerase 3, chloroplastic	68.223%	Swiss-Prot	strong database homology

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