LXL04_018896 | RubberDandelionOmics

Gene overview

LXL04_018896

Reference: OH-1004 Chr: Chr04 Coordinates: 19798110-19799763 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

735 bp · LXL04_018896|LXL04_018896|OH1004|cDNA

ATGGCGGAGATGGCGGTCGGCGGCGACGTTCCAACGAATAACACCATATACATCAACAATCTGAACGAGAAAACAAAACTTGATGAGTTAAAGAAATCGCTGCAAGCTGTGTTCTCGCAATTTGGCAAAATCCTGGAGATACTTGCGTTTAAAACCCTAAAACACAAGGGTCAAGCGTGGGTTGTTTTTGAGGACGTTTCATCCGCCACCAGTGCCCTCAAGCAGATGCAGGGCTTTCCATTCTACGACAAACCTATGAG...

CDS

Download CDS FASTA

735 bp · LXL04_018896|LXL04_018896|OH1004|CDS

ATGGCGGAGATGGCGGTCGGCGGCGACGTTCCAACGAATAACACCATATACATCAACAATCTGAACGAGAAAACAAAACTTGATGAGTTAAAGAAATCGCTGCAAGCTGTGTTCTCGCAATTTGGCAAAATCCTGGAGATACTTGCGTTTAAAACCCTAAAACACAAGGGTCAAGCGTGGGTTGTTTTTGAGGACGTTTCATCCGCCACCAGTGCCCTCAAGCAGATGCAGGGCTTTCCATTCTACGACAAACCTATGAG...

Protein

Download Protein FASTA

244 aa · LXL04_018896|LXL04_018896|OH1004|PROTEIN

MAEMAVGGDVPTNNTIYINNLNEKTKLDELKKSLQAVFSQFGKILEILAFKTLKHKGQAWVVFEDVSSATSALKQMQGFPFYDKPMRIQYAKTKSDVIAKSDGTFVPRERRKRHEEKGKKRKGQHDGNQAAVVNQGYAGAYGGPPPLSQLPYMGGGAKSGMPEAPAPPNSILFVQKLPHQTSSMMLQMLFGQHQGFKEVRMVEAKPGIAFIEYGDEMQATVAMHSLQGFKINPDSPMLITYAKK

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_018896`
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_018896

Location Chr04:19798110-19799763 (-)

Description Similar to U1A: U1 small nuclear ribonucleoprotein A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g47580`	Involved in nuclear pre-mRNA splicing (By similarity).	No verified direct reference in this release
`At2g30260`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release
`At1g06960`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0154800`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release
`UniProt: A2Y0J7`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018896 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000354 cis assembly of pre-catalytic spliceosome Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009631 cold acclimation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005685 U1 snRNP Cellular Component

GO:0005686 U2 snRNP Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G06960

ath:AT2G30260

ath:AT2G47580

dosa:Os05g0154800

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.

Nucleus0.845

Rank 1 · LXL04_018896 · OH-1004

Cytoplasm0.354

Rank 2 · LXL04_018896 · OH-1004

Cell membrane0.043

Rank 3 · LXL04_018896 · OH-1004

Mitochondrion0.027

Rank 4 · LXL04_018896 · OH-1004

Endoplasmic reticulum0.025

Rank 5 · LXL04_018896 · 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_116-86 aa

PF13893.13RRM_5153-232 aa

PF00076.29RRM_1172-232 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018896	`PF00076.29`	RRM_1	16	86	3.9e-23	81.8
LXL04_018896	`PF13893.13`	RRM_5	153	232	7.7e-12	45.7
LXL04_018896	`PF00076.29`	RRM_1	172	232	3.9e-23	81.8

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
`Q39244`	Arabidopsis thaliana	U1 small nuclear ribonucleoprotein A	71.074%	Swiss-Prot	strong database homology
`O22922`	Arabidopsis thaliana	U2 small nuclear ribonucleoprotein B''	53.333%	Swiss-Prot	strong database homology
`Q8H1S6`	Arabidopsis thaliana	U2 small nuclear ribonucleoprotein B'' 2	50.628%	Swiss-Prot	strong database homology
`Q0DKM4`	Oryza sativa subsp. japonica	U1 small nuclear ribonucleoprotein A	69.880%	Swiss-Prot	strong database homology
`A2Y0J7`	Oryza sativa subsp. indica	U1 small nuclear ribonucleoprotein A	69.880%	Swiss-Prot	strong database homology

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