LXL04_018163 | RubberDandelionOmics

Gene overview

LXL04_018163

Reference: OH-1004 Chr: Chr04 Coordinates: 7879873-7883423 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2217 bp · LXL04_018163|LXL04_018163|OH1004|cDNA

ATGGCCGGAGGGAGTAATAAGAAAAAAATCAATAAATCGAAAACTCGAAAACCCACCAAACAATCTTTGTTCGTGGAGGGTGGTTTGTTATCTGATTGGTCCCCTATCATCACTTCTCCTCCTTCCAGAGGAAAGAGTACTCATCCAATCGGTTCTGGGAATAAATTTAATGCATCTAAGAACAAATCTGCAGTGAAATATGAGATTGGTAGTACTTCTGGGGGTAAATCAAAAGCTACTCCCTCTACTTCGAGGATAGT...

CDS

Download CDS FASTA

2217 bp · LXL04_018163|LXL04_018163|OH1004|CDS

ATGGCCGGAGGGAGTAATAAGAAAAAAATCAATAAATCGAAAACTCGAAAACCCACCAAACAATCTTTGTTCGTGGAGGGTGGTTTGTTATCTGATTGGTCCCCTATCATCACTTCTCCTCCTTCCAGAGGAAAGAGTACTCATCCAATCGGTTCTGGGAATAAATTTAATGCATCTAAGAACAAATCTGCAGTGAAATATGAGATTGGTAGTACTTCTGGGGGTAAATCAAAAGCTACTCCCTCTACTTCGAGGATAGT...

Protein

Download Protein FASTA

738 aa · LXL04_018163|LXL04_018163|OH1004|PROTEIN

MAGGSNKKKINKSKTRKPTKQSLFVEGGLLSDWSPIITSPPSRGKSTHPIGSGNKFNASKNKSAVKYEIGSTSGGKSKATPSTSRIVDSRKPKANAFAYKYPQASSFTEEGGDGHNKFDKSNPIVLLDSKESKIIAYMDETPVSDSQTVKYTYDYGASFEVDDNDSPHTGLGFHDEEAEENPSFIEPSPVIEKQECSRFDSSSSHEMETDMMDDDGDGDGDGDDDSSSSPVTNSGFLSIGGMKLYTHDISDYEDDDNDDD...

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_018163`
TK1151 ID	TkA08G022980
OH-1004 ID	LXL04_018163
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.000
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_018163

Location Chr04:7879873-7883423 (-)

Description Similar to v1g244155: Zinc finger CCCH-type with G patch domain-containing protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g17070`	Involved in pre-mRNA splicing, specifically in spliceosome disassembly during late-stage splicing events (By similarity).	Mutation of Arabidopsis spliceosomal timekeeper locus1 causes circadian clock defects.2012 · DOI: 10.1105/tpc.112.104828

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018163 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0000390 spliceosomal complex disassembly Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0042752 regulation of circadian rhythm Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0031981 nuclear lumen Cellular Component

GO:0071008 U2-type post-mRNA release spliceosomal complex Cellular Component

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific Molecular Function

KEGG gene cross-reference

ath:AT1G17070

hsa:55105

mmu:67769

nve:5510508

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.

Nucleus0.810

Rank 1 · LXL04_018163 · OH-1004

Cytoplasm0.245

Rank 2 · LXL04_018163 · OH-1004

Cell membrane0.073

Rank 3 · LXL04_018163 · OH-1004

Endoplasmic reticulum0.056

Rank 4 · LXL04_018163 · OH-1004

Plastid0.018

Rank 5 · LXL04_018163 · 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.

PF01424.29R3H437-495 aa

PF01585.29G-patch610-654 aa

PF12656.13G-patch_2612-655 aa

PF01585.29G-patch693-737 aa

PF12656.13G-patch_2695-737 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018163	`PF01424.29`	R3H	437	495	1.4e-07	32.1
LXL04_018163	`PF01585.29`	G-patch	610	654	1.4e-30	105.7
LXL04_018163	`PF12656.13`	G-patch_2	612	655	6.2e-15	55.7
LXL04_018163	`PF01585.29`	G-patch	693	737	1.4e-30	105.7
LXL04_018163	`PF12656.13`	G-patch_2	695	737	6.2e-15	55.7

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
`Q9SHG6`	Arabidopsis thaliana	Septin and tuftelin-interacting protein 1 homolog 1	38.636%	Swiss-Prot	weak database homology

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