LXL04_001257 | RubberDandelionOmics

Gene overview

LXL04_001257

Reference: OH-1004 Chr: Chr01 Coordinates: 22957786-22961309 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1005 bp · LXL04_001257|LXL04_001257|OH1004|cDNA

GATCCAAATAATTTGTTCGCCCGAAGTAGTGGTCTTGTTGTCCACTGCTTAAAGGAACTCGAACCTTCCAGGCTTCCACGACTGCGTTTTCTACTTTTCTTATTTGTCGCTCCTAAATTTCCGAAGATCATCacattttttttcctttttcaAAAACATGGGCCGCTCAAGTCGCACTCTCTATGTGGGTAATCTCCCTGGTGATATTCGTGAAAGAGAAATTGAAGATTTGTTTTACAAGTATGGTCCAATTGTTGAAA...

CDS

Download CDS FASTA

891 bp · LXL04_001257|LXL04_001257|OH1004|CDS

TTGTCGCTCCTAAATTTCCGAAGATCATCACATTTTTTTTCCTTTTTCAAAAACATGGGCCGCTCAAGTCGCACTCTCTATGTGGGTAATCTCCCTGGTGATATTCGTGAAAGAGAAATTGAAGATTTGTTTTACAAGTATGGTCCAATTGTTGAAATCGAATTGAAAATTCCACCTAGACCCCCTAGCTTTGCCTTTGTAGAGTTTGAAGATTCTCGTGATGCTGAAGATGCGATTCATGGACGTGACGGCTATAAGTT...

Protein

Download Protein FASTA

296 aa · LXL04_001257|LXL04_001257|OH1004|PROTEIN

MSLLNFRRSSHFFSFFKNMGRSSRTLYVGNLPGDIREREIEDLFYKYGPIVEIELKIPPRPPSFAFVEFEDSRDAEDAIHGRDGYKFDGHRLRVELAHGGRVSSSSIDRHTSSHRESSRRSDYRVYVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRDGMRGIVDYTNYDDMKYAIRKLDDSLFRNQFSKAYIRVEEYDRRSRSPSPYYSRSRSPTHSRSRSYSPRDKYSRRSRSRSMWIPRRSCGLHHVILGAKVGCL...

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_001257`
TK1151 ID	TkA01G551180
OH-1004 ID	LXL04_001257
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.100
Protein coverage (%)	TK1151 71.028 / OH-1004 77.027 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_001257

Location Chr01:22957786-22961309 (-)

Description Similar to SR30: Serine/arginine-rich splicing factor SR30

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g09140`	Regulatory splicing factor that modulates alternative splicing and gene expression in specific cell types.	atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.1999 · DOI: 10.1101/gad.13.8.987
`At1g02840`	General splicing factor.	atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.1999 · DOI: 10.1101/gad.13.8.987
`At4g02430`	Probably involved in intron recognition and spliceosome assembly.	No verified direct reference in this release
`At3g49430`	Probably involved in intron recognition and spliceosome assembly.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001257 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0035061 interchromatin granule Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G02840

ath:AT1G09140

ath:AT3G49430

ath:AT4G02430

gga:772264

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.

Nucleus0.902

Rank 1 · LXL04_001257 · OH-1004

Cytoplasm0.285

Rank 2 · LXL04_001257 · OH-1004

Cell membrane0.022

Rank 3 · LXL04_001257 · OH-1004

Mitochondrion0.015

Rank 4 · LXL04_001257 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_001257 · 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_126-93 aa

PF00076.29RRM_1125-188 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001257	`PF00076.29`	RRM_1	26	93	7.2e-32	109.8
LXL04_001257	`PF00076.29`	RRM_1	125	188	7.2e-32	109.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9XFR5`	Arabidopsis thaliana	Serine/arginine-rich splicing factor SR30	74.346%	Swiss-Prot	moderate database homology
`O22315`	Arabidopsis thaliana	Serine/arginine-rich-splicing factor SR34	67.662%	Swiss-Prot	moderate database homology
`F4JHI7`	Arabidopsis thaliana	Serine/arginine-rich splicing factor SR34B	68.041%	Swiss-Prot	moderate database homology
`A2RVS6`	Arabidopsis thaliana	Serine/arginine-rich splicing factor SR34A	65.990%	Swiss-Prot	moderate database homology

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