LXL04_027230 | RubberDandelionOmics

Gene overview

LXL04_027230

Reference: OH-1004 Chr: Chr06 Coordinates: 11351874-11357170 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2838 bp · LXL04_027230|LXL04_027230|OH1004|cDNA

ATGTATAAATCGGTGGTGGCTGTTTATGATGGTGAAAAAGTCATCGGTGATGTTGAGGTTTATTTTAATCCTCATCTGATGAATCTGAATATGAGAGAGAAACTGAAAGACAAAATCAGGATTTCGTACTATTCGACACCAAGTGAGAGGTGCTCGCCACTTGCTGTTCTTCACACAATTACTTCACCAACAACTGGGGTTTGCTTGAAAATGGAGTCCAGCAAAACCATCAACTCGAACTCGCAGCTCAACCTTTTGCA...

CDS

Download CDS FASTA

2838 bp · LXL04_027230|LXL04_027230|OH1004|CDS

ATGTATAAATCGGTGGTGGCTGTTTATGATGGTGAAAAAGTCATCGGTGATGTTGAGGTTTATTTTAATCCTCATCTGATGAATCTGAATATGAGAGAGAAACTGAAAGACAAAATCAGGATTTCGTACTATTCGACACCAAGTGAGAGGTGCTCGCCACTTGCTGTTCTTCACACAATTACTTCACCAACAACTGGGGTTTGCTTGAAAATGGAGTCCAGCAAAACCATCAACTCGAACTCGCAGCTCAACCTTTTGCA...

Protein

Download Protein FASTA

945 aa · LXL04_027230|LXL04_027230|OH1004|PROTEIN

MYKSVVAVYDGEKVIGDVEVYFNPHLMNLNMREKLKDKIRISYYSTPSERCSPLAVLHTITSPTTGVCLKMESSKTINSNSQLNLLHSTCLRENKTAVVSYGGEELHLVAMRSRRNDMFPCFWGFSIPPGLYESCLVMLNLRCLGIVFDLDETLIVANTLRSFEDRIEALQRKVNCEVDPQRVAGMLGEIKRYQDDRNILKQYADSDQVVDNGKILKAQSEVVPPLSDNHQPLVRPLIRLQDKNIILTRINPLIRDTSVL...

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_027230`
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_027230

Location Chr06:11351874-11357170 (+)

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
`At5g01270`	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).	Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases.2004 · DOI: 10.1073/pnas.0403174101 The Arabidopsis thaliana carboxyl-terminal domain phosphatase-like 2 regulates plant growth, stress and auxin responses.2008 · DOI: 10.1007/s11103-008-9348-y A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis .2017 · DOI: 10.1073/pnas.1710683114 Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis.2020 · DOI: 10.1038/s41467-020-20089-0

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027230 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006351 DNA-templated transcription Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009611 response to wounding Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0034244 negative regulation of transcription elongation by RNA polymerase II Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

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

KEGG gene cross-reference

ath:AT4G21670

ath:AT5G01270

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.

Nucleus0.611

Rank 1 · LXL04_027230 · OH-1004

Cytoplasm0.427

Rank 2 · LXL04_027230 · OH-1004

Cell membrane0.052

Rank 3 · LXL04_027230 · OH-1004

Mitochondrion0.048

Rank 4 · LXL04_027230 · OH-1004

Endoplasmic reticulum0.037

Rank 5 · LXL04_027230 · 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.

PF28898.1SPOC_CPL1_21-126 aa

PF03031.25NIF254-358 aa

PF00035.33dsrm717-756 aa

PF00035.33dsrm829-891 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027230	`PF28898.1`	SPOC_CPL1_2	1	126	9.6e-44	149.1
LXL04_027230	`PF03031.25`	NIF	254	358	3.3e-09	37.3
LXL04_027230	`PF00035.33`	dsrm	717	756	2e-14	54.6
LXL04_027230	`PF00035.33`	dsrm	829	891	2e-14	54.6

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
`Q5YDB6`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 1	53.500%	Swiss-Prot	strong database homology
`Q5YDB5`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 2	46.304%	Swiss-Prot	moderate database homology

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