LXL04_020815 | RubberDandelionOmics

Gene overview

LXL04_020815

Reference: OH-1004 Chr: Chr04 Coordinates: 110021403-110025115 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2142 bp · LXL04_020815|LXL04_020815|OH1004|cDNA

ATGGAGATGCAGTCAATAAGGCTTCGTTTGGTGTTCGAAGATCGTTCGGTTCTTAACGAAACCCAGCTATCCGACGGTATGAACCAGAGCTGGCTTCTAATTGAACCAGCCAAACATCGGAAAATCTCTGATGTCTGCAATCATCTTCTTCACATTTTCGACCTTCGTCGGTCGTGCCCTAATGGGATCCTCTTATATGTAATTCTCTCTCCCTATATACCCCAATTTATCGATACTGAGGCAGTAAGAAACACAAAGCC...

CDS

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2142 bp · LXL04_020815|LXL04_020815|OH1004|CDS

ATGGAGATGCAGTCAATAAGGCTTCGTTTGGTGTTCGAAGATCGTTCGGTTCTTAACGAAACCCAGCTATCCGACGGTATGAACCAGAGCTGGCTTCTAATTGAACCAGCCAAACATCGGAAAATCTCTGATGTCTGCAATCATCTTCTTCACATTTTCGACCTTCGTCGGTCGTGCCCTAATGGGATCCTCTTATATGTAATTCTCTCTCCCTATATACCCCAATTTATCGATACTGAGGCAGTAAGAAACACAAAGCC...

Protein

Download Protein FASTA

713 aa · LXL04_020815|LXL04_020815|OH1004|PROTEIN

MEMQSIRLRLVFEDRSVLNETQLSDGMNQSWLLIEPAKHRKISDVCNHLLHIFDLRRSCPNGILLYVILSPYIPQFIDTEAVRNTKPNSTLNYICVKMESFVLPPSESTRILKDKEILCVKRKETAFTEAIEGADVDNLLGYDEVNRKEPVNNGMLLLANEEFDKETGGYKSESEEEKLEDEPSPIETASKKRKASTKTRSSKKKKHRSVKDGFEDEVVTEDNNIKNDESCPMKVTKPNKEKGSAETVIVKVISPLKVKR...

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_020815`
TK1151 ID	TkA05G312960
OH-1004 ID	LXL04_020815
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	87.200
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_020815

Location Chr04:110021403-110025115 (+)

Description Similar to COIL: Coilin

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g13030`	Probable component of nuclear coiled bodies, also known as Cajal bodies or CBs, which are involved in the modification and assembly of nucleoplasmic snRNPs (Probable).	A distant coilin homologue is required for the formation of cajal bodies in Arabidopsis.2006 · DOI: 10.1091/mbc.e05-12-1157

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_020815 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0006396 RNA processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0015030 Cajal body Cellular Component

GO:0030619 U1 snRNA binding Molecular Function

GO:0030620 U2 snRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G13030

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.

Nucleus0.922

Rank 1 · LXL04_020815 · OH-1004

Cytoplasm0.148

Rank 2 · LXL04_020815 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_020815 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_020815 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_020815 · 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.

PF15862.11Coilin_N97-227 aa

PF23086.2Tudor_Coilin521-621 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_020815	`PF15862.11`	Coilin_N	97	227	2.8e-13	50.7
LXL04_020815	`PF23086.2`	Tudor_Coilin	521	621	3.8e-39	133.8

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
`Q8RWK8`	Arabidopsis thaliana	Coilin	41.429%	Swiss-Prot	weak database homology

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