LXL04_017807 | RubberDandelionOmics

Gene overview

LXL04_017807

Reference: OH-1004 Chr: Chr04 Coordinates: 1513530-1516850 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1187 bp · LXL04_017807|LXL04_017807|OH1004|cDNA

ATGTCGTTCATGTATAATCCTGACCATTTAAAAACGCATGCTGGATCAGTCCCTTTCGTCCCTAAAGGCATTGAAGTTGATGGGAAGACTGTTGTTACTAGTGATCATGCTTTAGAACTGGAATTTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGATACATTGGTCTTGAATTAAGTGATATGTACACAGCACTTGGTAGTCAGGAGTATTTGCTACCAAGGGACCAAACCGCCAGTGAGCCGCCTCAGTTTCCGGT...

CDS

Download CDS FASTA

1182 bp · LXL04_017807|LXL04_017807|OH1004|CDS

ATGTCGTTCATGTATAATCCTGACCATTTAAAAACGCATGCTGGATCAGTCCCTTTCGTCCCTAAAGGCATTGAAGTTGATGGGAAGACTGTTGTTACTAGTGATCATGCTTTAGAACTGGAATTTGTTCCTGATTGGATAGCCATTGTAGGAAGTGGATACATTGGTCTTGAATTAAGTGATATGTACACAGCACTTGGTAGTCAGGAGTATTTGCTACCAAGGGACCAAACCGCCAGTGAGCCGCCTCAGTTTCCGGT...

Protein

Download Protein FASTA

393 aa · LXL04_017807|LXL04_017807|OH1004|PROTEIN

MSFMYNPDHLKTHAGSVPFVPKGIEVDGKTVVTSDHALELEFVPDWIAIVGSGYIGLELSDMYTALGSQEYLLPRDQTASEPPQFPVRPPPPPMQVFAPRVEPPPHGGWFPMGSRQMNRRPVSVPVPLHSESMHIHKKHSLRAPPFVHKVESSLLPKEAFQRDDRLRLSHSSSVFPPFPGEESSMGQSLSSSRDMEIEGGNNDNFNESPSEYLHYIAFKCGTKVEFRQALTPSVDLQFSVEKIGEGNGRTRREAQHEVAE...

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_017807`
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_017807

Location Chr04:1513530-1516850 (-)

Description Similar to CPL1: RNA polymerase II C-terminal domain phosphatase-like 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21670`	Processively dephosphorylates 'Ser-5' but not 'Ser-2' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit (RPB1).	Fusion genetic analysis of jasmonate-signalling mutants in Arabidopsis.2002 · DOI: 10.1046/j.0960-7412.2001.01241.x C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development.2002 · DOI: 10.1073/pnas.112276199 Repression of stress-responsive genes by FIERY2, a novel transcriptional regulator in Arabidopsis.2002 · DOI: 10.1073/pnas.162111599 Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases.2004 · DOI: 10.1073/pnas.0403174101 CTD phosphatases in the attenuation of wound-induced transcription of jasmonic acid biosynthetic genes in Arabidopsis.2009 · DOI: 10.1111/j.1365-313x.2008.03663.x The arabidopsis RNA binding protein with K homology motifs, SHINY1, interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress stress-inducible gene expression.2013 · DOI: 10.1371/journal.pgen.1003625 The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.2015 · DOI: 10.1093/nar/gkv751 The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis.2016 · DOI: 10.1105/tpc.15.00771
`At4g16155`	Lipoamide dehydrogenase is a component of the plastidial pyruvate dehydrogenase complex (PDC).	No verified direct reference in this release
`At3g16950`	Lipoamide dehydrogenase is a component of the plastidial pyruvate dehydrogenase complex (PDC).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_017807 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0006086 pyruvate decarboxylation to acetyl-CoA Biological Process

GO:0006103 2-oxoglutarate metabolic process Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009611 response to wounding Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0046685 response to arsenic-containing substance Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT3G16950

ath:AT4G16155

ath:AT4G21670

hma:rrnAC2953

syn:slr1096

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.

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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.

Nucleus0.836

Rank 1 · LXL04_017807 · OH-1004

Cytoplasm0.271

Rank 2 · LXL04_017807 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_017807 · OH-1004

Endoplasmic reticulum0.023

Rank 4 · LXL04_017807 · OH-1004

Mitochondrion0.022

Rank 5 · LXL04_017807 · 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.

PF07992.21Pyr_redox_215-74 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017807	`PF07992.21`	Pyr_redox_2	15	74	7.6e-07	29.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q5YDB6`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 1	40.092%	Swiss-Prot	weak database homology
`F4JLP5`	Arabidopsis thaliana	Dihydrolipoyl dehydrogenase 2, chloroplastic	89.091%	Swiss-Prot	weak database homology
`A8MS68`	Arabidopsis thaliana	Dihydrolipoyl dehydrogenase 1, chloroplastic	71.831%	Swiss-Prot	weak database homology

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