LXL04_015253 | RubberDandelionOmics

Gene overview

LXL04_015253

Reference: OH-1004 Chr: Chr03 Coordinates: 66914819-66917299 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1431 bp · LXL04_015253|LXL04_015253|OH1004|cDNA

ATGAGTCGCATTGATGATTCACCGGTGAACTCATCAAGCAGCGATGATTTTGCCGCATTTCTGGATGCTGAGCTAGATTCTGTTTCTGATAGTTCCCCTCAATCagaagaagaagtagaagaagaagaggaacaagaagaagaagtagCAGAAGAGGAAgacgaagaagatgatgatggtgatgatgagaATTGTAAGTATCCTATTGAAAGGACTAAAAGGAGGAAGATCAGTTTTTCTGAAAGTACCCAAGAACCCAA...

CDS

Download CDS FASTA

1431 bp · LXL04_015253|LXL04_015253|OH1004|CDS

ATGAGTCGCATTGATGATTCACCGGTGAACTCATCAAGCAGCGATGATTTTGCCGCATTTCTGGATGCTGAGCTAGATTCTGTTTCTGATAGTTCCCCTCAATCAGAAGAAGAAGTAGAAGAAGAAGAGGAACAAGAAGAAGAAGTAGCAGAAGAGGAAGACGAAGAAGATGATGATGGTGATGATGAGAATTGTAAGTATCCTATTGAAAGGACTAAAAGGAGGAAGATCAGTTTTTCTGAAAGTACCCAAGAACCCAA...

Protein

Download Protein FASTA

476 aa · LXL04_015253|LXL04_015253|OH1004|PROTEIN

MSRIDDSPVNSSSSDDFAAFLDAELDSVSDSSPQSEEEVEEEEEQEEEVAEEEDEEDDDGDDENCKYPIERTKRRKISFSESTQEPNGSTSHTEQEIILESVKEDICAHPGFIGGMCIKCGEKMDTDNQSGVAFGYIHKDLRLANDEIARLRDRDLKNLLRHKKLYLVLDLDHTLLNSSRMSDIIQEEGYLMNQNDPVQDALKDSLFKLPSMHMVTKLRPFVRTFLKEASKLFEMYIYTMGERSYALEMANLLDPGRVYF...

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_015253`
TK1151 ID	TkA02G351720
OH-1004 ID	LXL04_015253
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.500
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_015253

Location Chr03:66914819-66917299 (-)

Description Similar to CPL4: RNA polymerase II C-terminal domain phosphatase-like 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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

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Functional annotation source: OH1004 · LXL04_015253 · 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.

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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.

Nucleus0.761

Rank 1 · LXL04_015253 · OH-1004

Cytoplasm0.290

Rank 2 · LXL04_015253 · OH-1004

Cell membrane0.058

Rank 3 · LXL04_015253 · OH-1004

Endoplasmic reticulum0.035

Rank 4 · LXL04_015253 · OH-1004

Mitochondrion0.023

Rank 5 · LXL04_015253 · 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.

PF03031.25NIF166-316 aa

PF00533.34BRCT379-453 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015253	`PF03031.25`	NIF	166	316	4.4e-26	92.2
LXL04_015253	`PF00533.34`	BRCT	379	453	9.9e-06	26.4

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
`Q00IB6`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 4	54.565%	Swiss-Prot	strong database homology
`Q8LL04`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 3	40.896%	Swiss-Prot	moderate database homology
`F4JCB2`	Arabidopsis thaliana	RNA polymerase II C-terminal domain phosphatase-like 5	40.942%	Swiss-Prot	moderate database homology

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