LXL04_027086 | RubberDandelionOmics

Gene overview

LXL04_027086

Reference: OH-1004 Chr: Chr06 Coordinates: 8569443-8573107 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1239 bp · LXL04_027086|LXL04_027086|OH1004|cDNA

ATGCAACCTGCAACAACCCCGCTTATGGACCCTCAGTACCAGCAACAACAGTGGATGATGATGAatcaacaacaaccacaaccaccGCAACAACAGTTTCAGCAACAACCACCGGTACAGCAAATGTATAATTACAACCAGCAACCACCACAGGCTGCCGCAATTCCACCTCAGTACACGGCACCCGCGGTAGCACCGGCTGGTGGAGCGACTCCTCAACCAGCTAGCGCGGATGAGATCCGTACCCTATGGATCGGCGA...

CDS

Download CDS FASTA

1239 bp · LXL04_027086|LXL04_027086|OH1004|CDS

ATGCAACCTGCAACAACCCCGCTTATGGACCCTCAGTACCAGCAACAACAGTGGATGATGATGAATCAACAACAACCACAACCACCGCAACAACAGTTTCAGCAACAACCACCGGTACAGCAAATGTATAATTACAACCAGCAACCACCACAGGCTGCCGCAATTCCACCTCAGTACACGGCACCCGCGGTAGCACCGGCTGGTGGAGCGACTCCTCAACCAGCTAGCGCGGATGAGATCCGTACCCTATGGATCGGCGA...

Protein

Download Protein FASTA

412 aa · LXL04_027086|LXL04_027086|OH1004|PROTEIN

MQPATTPLMDPQYQQQQWMMMNQQQPQPPQQQFQQQPPVQQMYNYNQQPPQAAAIPPQYTAPAVAPAGGATPQPASADEIRTLWIGDLQYWMDEQYLLSCFAQTGEVVSAKVIRNKQSGQSEGYGFIEFVNRAAAERHLQAYNGTLMPNVEQLFRLNWATFGAGEKRQDDTPDYTIFVGDLAADVTDYTLQETFRAHYPSVKGAKVVTDRLTGRTKGYGFVKFGDESEQVRAMTEMNGRLCSTRPMRIGPAANKKNMASQ...

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_027086`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_027086

Location Chr06:8569443-8573107 (+)

Description Similar to RBP45: Polyadenylate-binding protein RBP45

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g11650`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	Phylogenetic and expression analysis of RNA-binding proteins with triple RNA recognition motifs in plants.2011 · DOI: 10.1007/s10059-011-0001-2
`At4g27000`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At5g54900`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0625800`	RNA-binding protein that binds to a cis-localization element or zipcode, within the 5'-CDS of prolamine RNA.	Targeted Endoplasmic Reticulum Localization of Storage Protein mRNAs Requires the RNA-Binding Protein RBP-L.2019 · DOI: 10.1104/pp.18.01434 Zipcode RNA-Binding Proteins and Membrane Trafficking Proteins Cooperate to Transport Glutelin mRNAs in Rice Endosperm.2020 · DOI: 10.1105/tpc.20.00111

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027086 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0010193 response to ozone Biological Process

GO:0051028 mRNA transport Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008143 poly(A) binding Molecular Function

KEGG gene cross-reference

ath:AT1G11650

ath:AT4G27000

ath:AT5G54900

dosa:Os04g0625800

osa:4337064

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.781

Rank 1 · LXL04_027086 · OH-1004

Cytoplasm0.442

Rank 2 · LXL04_027086 · OH-1004

Cell membrane0.040

Rank 3 · LXL04_027086 · OH-1004

Endoplasmic reticulum0.030

Rank 4 · LXL04_027086 · OH-1004

Mitochondrion0.023

Rank 5 · LXL04_027086 · 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.

PF00076.29RRM_183-148 aa

PF00076.29RRM_1176-244 aa

PF13893.13RRM_5276-360 aa

PF00076.29RRM_1284-348 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027086	`PF00076.29`	RRM_1	83	148	2.8e-49	165.6
LXL04_027086	`PF00076.29`	RRM_1	176	244	2.8e-49	165.6
LXL04_027086	`PF13893.13`	RRM_5	276	360	3.5e-07	30.7
LXL04_027086	`PF00076.29`	RRM_1	284	348	2.8e-49	165.6

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
`Q9SAB3`	Arabidopsis thaliana	Polyadenylate-binding protein RBP45B	67.042%	Swiss-Prot	strong database homology
`Q93W34`	Arabidopsis thaliana	Polyadenylate-binding protein RBP45C	66.562%	Swiss-Prot	strong database homology
`Q9FPJ8`	Arabidopsis thaliana	Polyadenylate-binding protein RBP45A	65.732%	Swiss-Prot	strong database homology
`Q0J9Y2`	Oryza sativa subsp. japonica	RNA-binding protein L	68.769%	Swiss-Prot	strong database homology

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