LXL04_011557 | RubberDandelionOmics

Gene overview

LXL04_011557

Reference: OH-1004 Chr: Chr02 Coordinates: 167246492-167247890 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

654 bp · LXL04_011557|LXL04_011557|OH1004|cDNA

ATGTCTCGTGTGTATGTTGGGAACCTGGATCCACGAGTTTCCGAGCGAGAGCTTGAAGATGAGTTTCGCGTCTACGGTGTTCTAAGGAATGTGTGGGTTGCTAGAAGGCCACCTGGCTATGCATTTGTTGAATTTGATGATCGCAGAGACGCACTGGATGCTATTCGTGCACTGGACGGGAAGAACGGGTGGCGTGTAGAGCTATCTCACAATTCAAAGGAAGGTGGAGGAGGCGGCCGTGGTGGTGGTCGTGGACGCGG...

CDS

Download CDS FASTA

654 bp · LXL04_011557|LXL04_011557|OH1004|CDS

ATGTCTCGTGTGTATGTTGGGAACCTGGATCCACGAGTTTCCGAGCGAGAGCTTGAAGATGAGTTTCGCGTCTACGGTGTTCTAAGGAATGTGTGGGTTGCTAGAAGGCCACCTGGCTATGCATTTGTTGAATTTGATGATCGCAGAGACGCACTGGATGCTATTCGTGCACTGGACGGGAAGAACGGGTGGCGTGTAGAGCTATCTCACAATTCAAAGGAAGGTGGAGGAGGCGGCCGTGGTGGTGGTCGTGGACGCGG...

Protein

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217 aa · LXL04_011557|LXL04_011557|OH1004|PROTEIN

MSRVYVGNLDPRVSERELEDEFRVYGVLRNVWVARRPPGYAFVEFDDRRDALDAIRALDGKNGWRVELSHNSKEGGGGGRGGGRGRGGGGDDLKCYECGEPGHFARECRLRVGPRGLGSGRRRSPSPRRRRSPSYGRRSYSPRYSPRGRRSPPRRSISPYRGRSRSPPPYRRARRDSPYANGYDFQSSVHYYANSMGASSVRYDGLELYRNGLNKVM

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_011557`
TK1151 ID	TkA03G601640
OH-1004 ID	LXL04_011557
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_011557

Location Chr02:167246492-167247890 (-)

Description Similar to RSZP21: Serine/arginine-rich splicing factor RSZ21

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g31580`	Sequence-specific RNA-binding protein probably involved in pre-mRNA splicing.	A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities.1999 · DOI: 10.1023/a:1006129615846
`At2g24590`	Probably involved in intron recognition and spliceosome assembly.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0789400`	Involved in pre-mRNA splicing.	No verified direct reference in this release
`Os06g0187900`	Involved in pre-mRNA splicing.	No verified direct reference in this release
`Os02g0610600`	Involved in pre-mRNA splicing.	The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA.2006 · DOI: 10.1105/tpc.105.037069

Functional annotation source

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Functional annotation source: OH1004 · LXL04_011557 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0000398 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:0005773 vacuole Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G24590

ath:AT4G31580

dosa:Os02g0610600

dosa:Os02g0789400

dosa:Os06g0187900

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.

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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.

Nucleus0.958

Rank 1 · LXL04_011557 · OH-1004

Cytoplasm0.220

Rank 2 · LXL04_011557 · OH-1004

Cell membrane0.016

Rank 3 · LXL04_011557 · OH-1004

Endoplasmic reticulum0.011

Rank 4 · LXL04_011557 · OH-1004

Mitochondrion0.010

Rank 5 · LXL04_011557 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00076.29RRM_14-61 aa

PF00098.29zf-CCHC94-109 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011557	`PF00076.29`	RRM_1	4	61	8e-16	58.4
LXL04_011557	`PF00098.29`	zf-CCHC	94	109	9.6e-08	32.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`O81126`	Arabidopsis thaliana	Serine/arginine-rich splicing factor RSZ22	66.316%	Swiss-Prot	strong database homology
`Q9SJA6`	Arabidopsis thaliana	Serine/arginine-rich splicing factor RSZ22A	65.775%	Swiss-Prot	strong database homology
`Q6K4N0`	Oryza sativa subsp. japonica	Serine/arginine-rich splicing factor RSZ21	61.579%	Swiss-Prot	strong database homology
`Q69KL9`	Oryza sativa subsp. japonica	Serine/arginine-rich splicing factor RSZ21A	64.398%	Swiss-Prot	strong database homology
`Q6K9C3`	Oryza sativa subsp. japonica	Serine/arginine-rich splicing factor RSZ23	73.451%	Swiss-Prot	moderate database homology

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