LXL04_032566 | RubberDandelionOmics

Gene overview

LXL04_032566

Reference: OH-1004 Chr: Chr07 Coordinates: 25620625-25622259 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1002 bp · LXL04_032566|LXL04_032566|OH1004|cDNA

ATGGCGGAGCACTTGGCCTCCATATTTGGTACGGAAAAGGACCGAGTCAACTGTCCTTTCTACTTCAAGATCGGAGCTTGTCGCCATGGAGATCGATGTTCTAGGCTCCACACCAAACCCAGCATCAGCCCTACCCTGTTGCTCTCCAACATGTATCAGCGTCCCGATATGATCACTCCAGGTGTTGATCCTCAAGGCCAGCCCCTTGATCCTAGCAAAATCCAGGATCACTTCGAGGATTTCTACGAAGATCTGTTTGA...

CDS

Download CDS FASTA

1002 bp · LXL04_032566|LXL04_032566|OH1004|CDS

ATGGCGGAGCACTTGGCCTCCATATTTGGTACGGAAAAGGACCGAGTCAACTGTCCTTTCTACTTCAAGATCGGAGCTTGTCGCCATGGAGATCGATGTTCTAGGCTCCACACCAAACCCAGCATCAGCCCTACCCTGTTGCTCTCCAACATGTATCAGCGTCCCGATATGATCACTCCAGGTGTTGATCCTCAAGGCCAGCCCCTTGATCCTAGCAAAATCCAGGATCACTTCGAGGATTTCTACGAAGATCTGTTTGA...

Protein

Download Protein FASTA

333 aa · LXL04_032566|LXL04_032566|OH1004|PROTEIN

MAEHLASIFGTEKDRVNCPFYFKIGACRHGDRCSRLHTKPSISPTLLLSNMYQRPDMITPGVDPQGQPLDPSKIQDHFEDFYEDLFEELGKYGEIESLNICDNLADHMVGNVYAQFREEEHAAAALQNLSGRFYAGRPIIVDFSPVTDFREATCRQYEENVCNRGGYCNFMHLKKINKDLRRQLFGRRRRSRSRSRSPPRHRNHDDRPQGGGGGGGGGRGYGRRGSGGYSDHRSSDRGRRPRSRSPGRRGGGGGRSRSPA...

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_032566`
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_032566

Location Chr07:25620625-25622259 (-)

Description Similar to U2AF35A: Splicing factor U2af small subunit A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g42820`	Necessary for the splicing of pre-mRNA (By similarity).	No verified direct reference in this release
`At1g27650`	Necessary for the splicing of pre-mRNA (By similarity).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0491756`	Necessary for the splicing of pre-mRNA.	No verified direct reference in this release
`Os05g0564200`	Necessary for the splicing of pre-mRNA.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032566 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0048573 photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0089701 U2AF complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0030628 pre-mRNA 3'-splice site binding Molecular Function

KEGG gene cross-reference

ath:AT1G27650

ath:AT5G42820

dosa:Os05g0564200

dosa:Os09g0491756

rno:361542

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.

Nucleus0.888

Rank 1 · LXL04_032566 · OH-1004

Cytoplasm0.268

Rank 2 · LXL04_032566 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_032566 · OH-1004

Mitochondrion0.016

Rank 4 · LXL04_032566 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_032566 · 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.

PF00642.31zf-CCCH14-37 aa

PF00076.29RRM_183-139 aa

PF29326.1RRM_MUD2_C106-150 aa

PF00642.31zf-CCCH150-173 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032566	`PF00642.31`	zf-CCCH	14	37	2.8e-12	46.9
LXL04_032566	`PF00076.29`	RRM_1	83	139	7.7e-06	26.4
LXL04_032566	`PF29326.1`	RRM_MUD2_C	106	150	2.2e-06	28.4
LXL04_032566	`PF00642.31`	zf-CCCH	150	173	2.8e-12	46.9

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
`Q9FMY5`	Arabidopsis thaliana	Splicing factor U2af small subunit B	68.966%	Swiss-Prot	strong database homology
`Q9S709`	Arabidopsis thaliana	Splicing factor U2af small subunit A	65.789%	Swiss-Prot	strong database homology
`Q9ZQW8`	Oryza sativa subsp. japonica	Splicing factor U2af small subunit A	66.102%	Swiss-Prot	strong database homology
`Q6AUG0`	Oryza sativa subsp. japonica	Splicing factor U2af small subunit B	78.919%	Swiss-Prot	moderate database homology

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