LXL04_018495 | RubberDandelionOmics

Gene overview

LXL04_018495

Reference: OH-1004 Chr: Chr04 Coordinates: 13766882-13768748 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1245 bp · LXL04_018495|LXL04_018495|OH1004|cDNA

ATGGCGGCTGAAACTGCAGCTGCTTCACATTTCCACTATCATTGCGGTTGGAGTCGGAGGAGATGCACCGCCGGATTCAAAACCCGACGCCGCCTGCCATTTCCACCGGCAGCTTCTTCTCAACCCATGGATATTCACACCAGCAATTCCTACAAAGAACTCGGTATGTTCTCGTTAAGAAAGAAGATAGAAGATTCCGTTAATCGAGCTGAAATTTTAGGCCTAACCGCATTGGAATTCGAAGAAACGCGACGAATCAA...

CDS

Download CDS FASTA

1245 bp · LXL04_018495|LXL04_018495|OH1004|CDS

ATGGCGGCTGAAACTGCAGCTGCTTCACATTTCCACTATCATTGCGGTTGGAGTCGGAGGAGATGCACCGCCGGATTCAAAACCCGACGCCGCCTGCCATTTCCACCGGCAGCTTCTTCTCAACCCATGGATATTCACACCAGCAATTCCTACAAAGAACTCGGTATGTTCTCGTTAAGAAAGAAGATAGAAGATTCCGTTAATCGAGCTGAAATTTTAGGCCTAACCGCATTGGAATTCGAAGAAACGCGACGAATCAA...

Protein

Download Protein FASTA

414 aa · LXL04_018495|LXL04_018495|OH1004|PROTEIN

MAAETAAASHFHYHCGWSRRRCTAGFKTRRRLPFPPAASSQPMDIHTSNSYKELGMFSLRKKIEDSVNRAEILGLTALEFEETRRIKQEEMIREYDLWDDLSKSSDILIKLADSAKVVDALKDLTYKVEEAKLITELAEMDIINYSLLKQAYTTSVDVSKFLDKYEMSKLLKGKYEFEGACVIIEAGSEGIRSEIWAEQLVGMYMKWAKKQGLKGRIIEKKCLSKSGGIKSAIIEFEYKYAYGYFLGEKGTHRMITSHPE...

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_018495`
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_018495

Location Chr04:13766882-13768748 (+)

Description Similar to PRFB3: Peptide chain release factor PrfB3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g57190`	Involved in the light- and stress-dependent regulation of stability of 3' processed petB transcripts, thus regulating cytochrome b6 accumulation, a rate-limiting step in photosynthetic electron transport.	Recruitment of a ribosomal release factor for light- and stress-dependent regulation of petB transcript stability in Arabidopsis chloroplasts.2011 · DOI: 10.1105/tpc.111.085324
`At5g36170`	Directs the termination of translation in response to the peptide chain termination codon UGA.	A peptide chain release factor 2 affects the stability of UGA-containing transcripts in Arabidopsis chloroplasts.2002 · DOI: 10.1105/tpc.006809

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018495 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006396 RNA processing Biological Process

GO:0006415 translational termination Biological Process

GO:0009657 plastid organization Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0043488 regulation of mRNA stability Biological Process

GO:0075523 viral translational frameshifting Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0003730 mRNA 3'-UTR binding Molecular Function

GO:0003747 translation release factor activity Molecular Function

GO:0016149 translation release factor activity, codon specific Molecular Function

KEGG gene cross-reference

ath:AT3G57190

ath:AT5G36170

cyp:PCC8801_3422

syn:sll1865

syw:SYNW2311

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.

Plastid0.830

Rank 1 · LXL04_018495 · OH-1004

Nucleus0.143

Rank 2 · LXL04_018495 · OH-1004

Mitochondrion0.071

Rank 3 · LXL04_018495 · OH-1004

Cytoplasm0.057

Rank 4 · LXL04_018495 · OH-1004

Peroxisome0.020

Rank 5 · LXL04_018495 · 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.

PF03462.24PCRF87-254 aa

PF00472.27RF-1303-380 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018495	`PF03462.24`	PCRF	87	254	6.2e-22	79.1
LXL04_018495	`PF00472.27`	RF-1	303	380	1.7e-10	41.6

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
`F4J264`	Arabidopsis thaliana	Peptide chain release factor PrfB3, chloroplastic	50.249%	Swiss-Prot	strong database homology
`Q9LVY0`	Arabidopsis thaliana	Peptide chain release factor PrfB1, chloroplastic	37.531%	Swiss-Prot	moderate database homology

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