LXL04_025720 | RubberDandelionOmics

Gene overview

LXL04_025720

Reference: OH-1004 Chr: Chr05 Coordinates: 115841402-115845474 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3318 bp · LXL04_025720|LXL04_025720|OH1004|cDNA

ATGGGGAAAGATTTATTGGTATCTGTAGGTGTGGATGTAGAGGAAGGTGAAATTTCGGATTCGGCGTCTATTGAAGAGATCAGTGCGGAGGATTTTGGTGTTAAGTCGCCGCCGGTTGGGACAGAGATTGCTGCTTCTAAGAATGCAGTCGATGATGATTCCAAGCAACAACAGCAGCAGCATCAGCAAGTTTGGACGATGCAGGATCTGTTAAAGTATCAGAATAAGTATCATAGGAATTACGCACCTGGCTTGTATAA...

CDS

Download CDS FASTA

3318 bp · LXL04_025720|LXL04_025720|OH1004|CDS

ATGGGGAAAGATTTATTGGTATCTGTAGGTGTGGATGTAGAGGAAGGTGAAATTTCGGATTCGGCGTCTATTGAAGAGATCAGTGCGGAGGATTTTGGTGTTAAGTCGCCGCCGGTTGGGACAGAGATTGCTGCTTCTAAGAATGCAGTCGATGATGATTCCAAGCAACAACAGCAGCAGCATCAGCAAGTTTGGACGATGCAGGATCTGTTAAAGTATCAGAATAAGTATCATAGGAATTACGCACCTGGCTTGTATAA...

Protein

Download Protein FASTA

1105 aa · LXL04_025720|LXL04_025720|OH1004|PROTEIN

MGKDLLVSVGVDVEEGEISDSASIEEISAEDFGVKSPPVGTEIAASKNAVDDDSKQQQQQHQQVWTMQDLLKYQNKYHRNYAPGLYNFAWAQAVQNKPLDDYLTTMNTSTPTDNNLKQPLLNDDNNNIEVKKEVTVNNDKDVVDISDDGESEKEEGELEEGEIDLDMEVVNAGKQGGVEDNVEKWINIIRIGLESITINDAKKSFTGVCSRLEDFLDSFSKLFLEKSISNKDDLGHLAFSSIQLVNSVYCSMSQTHKEQN...

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_025720`
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_025720

Location Chr05:115841402-115845474 (-)

Description Similar to CPL3: RNA polymerase II C-terminal domain phosphatase-like 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g33540`	Completely dephosphorylates 'Ser-2', and partially 'Ser-5' and 'Ser-7' of the heptad repeats YSPTSPS in the C-terminal domain (CTD) of the largest RNA polymerase II subunit (RPB1).	C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development.2002 · DOI: 10.1073/pnas.112276199 Arabidopsis carboxyl-terminal domain phosphatase-like isoforms share common catalytic and interaction domains but have distinct in planta functions.2006 · DOI: 10.1104/pp.106.084939 Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity.2014 · DOI: 10.1016/j.chom.2014.10.018 A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing.2019 · DOI: 10.1038/s41477-019-0419-7
`At5g58003`	Processively dephosphorylates 'Ser-2' and/or 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit (RPB1).	Arabidopsis carboxyl-terminal domain phosphatase-like isoforms share common catalytic and interaction domains but have distinct in planta functions.2006 · DOI: 10.1104/pp.106.084939
`At3g19600`	Mediates the dephosphorylation of 'Ser-2' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit (RPB1).	AtCPL5, a novel Ser-2-specific RNA polymerase II C-terminal domain phosphatase, positively regulates ABA and drought responses in Arabidopsis.2011 · DOI: 10.1111/j.1469-8137.2010.03601.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025720 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006952 defense response Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:1900369 negative regulation of post-transcriptional gene silencing by regulatory ncRNA Biological Process

GO:1902074 response to salt Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT2G33540

ath:AT3G19595

ath:AT3G19600

ath:AT5G58003

cel:CELE_F36F2.6

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.

Nucleus0.914

Rank 1 · LXL04_025720 · OH-1004

Cytoplasm0.179

Rank 2 · LXL04_025720 · OH-1004

Mitochondrion0.029

Rank 3 · LXL04_025720 · OH-1004

Cell membrane0.025

Rank 4 · LXL04_025720 · OH-1004

Endoplasmic reticulum0.013

Rank 5 · LXL04_025720 · 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.

PF25505.2ARM_CPL3186-307 aa

PF03031.25NIF796-948 aa

PF12738.14PTCB-BRCT1035-1085 aa

PF00533.34BRCT1040-1089 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025720	`PF25505.2`	ARM_CPL3	186	307	1.9e-41	141.5
LXL04_025720	`PF03031.25`	NIF	796	948	4.5e-23	82.4
LXL04_025720	`PF12738.14`	PTCB-BRCT	1035	1085	6.7e-06	26.7
LXL04_025720	`PF00533.34`	BRCT	1040	1089	2.1e-07	31.7

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
`Q8LL04`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 3	44.252%	Swiss-Prot	moderate database homology
`Q00IB6`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 4	44.785%	Swiss-Prot	weak database homology
`F4JCB2`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 5	33.796%	Swiss-Prot	weak database homology

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