LXL04_027623 | RubberDandelionOmics

Gene overview

LXL04_027623

Reference: OH-1004 Chr: Chr06 Coordinates: 20528091-20535363 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2505 bp · LXL04_027623|LXL04_027623|OH1004|cDNA

ATGATAATTGTTCTCCATTATTATGGAAGAACCGATGATCAAGAACTTGAAGAAAACCGGATTAACTTCAGTGACGTGAAGGTTGAAGATGGAGTTGATGTTGCTCTTTGTTTTTGGTTTACATGTGTTTGGATCGATGAGTTCTTGATGGGTATTGAAAGAGACGCTGAAGCCCTTCCAGCGATTCAGTTACCATTAAACACACATCTCCGTTCTCCATGTTCACCGGCGTCGTCGCCCTGCTCTGCCGCCGCCATCGA...

CDS

Download CDS FASTA

2505 bp · LXL04_027623|LXL04_027623|OH1004|CDS

ATGATAATTGTTCTCCATTATTATGGAAGAACCGATGATCAAGAACTTGAAGAAAACCGGATTAACTTCAGTGACGTGAAGGTTGAAGATGGAGTTGATGTTGCTCTTTGTTTTTGGTTTACATGTGTTTGGATCGATGAGTTCTTGATGGGTATTGAAAGAGACGCTGAAGCCCTTCCAGCGATTCAGTTACCATTAAACACACATCTCCGTTCTCCATGTTCACCGGCGTCGTCGCCCTGCTCTGCCGCCGCCATCGA...

Protein

Download Protein FASTA

834 aa · LXL04_027623|LXL04_027623|OH1004|PROTEIN

MIIVLHYYGRTDDQELEENRINFSDVKVEDGVDVALCFWFTCVWIDEFLMGIERDAEALPAIQLPLNTHLRSPCSPASSPCSAAAIDSATIAISNRLNSDGGKVSLQRRRWPIMASEEEEPREKTTGGDFLFLTGVGDHPEKMDDGEGGLSFDFEGGLDTAPTQPTASVPVIHQSTDNGPSASAANLSYSAAPPSAVNDPASAAAANANYPGRRSYRQTVCRHWLRSLCMKGEACGFLHQYDKSRMPICRFFRLYGECRE...

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_027623`
TK1151 ID	TkA07G079240
OH-1004 ID	LXL04_027623
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 82.974 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_027623

Location Chr06:20528091-20535363 (-)

Description Similar to CPSF30: 30-kDa cleavage and polyadenylation specificity factor 30

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g30460`	Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation.	Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.2006 · DOI: 10.1104/pp.105.070672 A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor.2007 · DOI: 10.1093/nar/gkm457 A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana.2008 · DOI: 10.1371/journal.pone.0002410 The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein.2010 · DOI: 10.1016/j.febslet.2010.03.007 Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis.2012 · DOI: 10.1105/tpc.112.096107 The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis.2014 · DOI: 10.1104/pp.114.236083

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0677700`	Zinc finger CCCH domain-containing protein 45.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027623 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006396 RNA processing Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0007286 spermatid development Biological Process

GO:0009626 plant-type hypersensitive response Biological Process

GO:0031124 mRNA 3'-end processing Biological Process

GO:0031440 regulation of mRNA 3'-end processing Biological Process

GO:0034052 positive regulation of plant-type hypersensitive response Biological Process

GO:0034612 response to tumor necrosis factor Biological Process

GO:0043068 positive regulation of programmed cell death Biological Process

GO:0044829 host-mediated activation of viral genome replication Biological Process

GO:0048024 regulation of mRNA splicing, via spliceosome Biological Process

KEGG gene cross-reference

ath:AT1G30460

dosa:Os06g0677700

hsa:64848

mmu:240255

pon:100173406

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.

Nucleus0.718

Rank 1 · LXL04_027623 · OH-1004

Cytoplasm0.404

Rank 2 · LXL04_027623 · OH-1004

Cell membrane0.039

Rank 3 · LXL04_027623 · OH-1004

Mitochondrion0.037

Rank 4 · LXL04_027623 · OH-1004

Endoplasmic reticulum0.037

Rank 5 · LXL04_027623 · 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.

PF04146.22YTH413-547 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027623	`PF04146.22`	YTH	413	547	2.5e-46	157.5

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
`A9LNK9`	Arabidopsis thaliana	30-kDa cleavage and polyadenylation specificity factor 30	63.188%	Swiss-Prot	strong database homology
`Q0DA50`	Oryza sativa subsp. japonica	Zinc finger CCCH domain-containing protein 45	54.610%	Swiss-Prot	strong database homology

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