LXL04_028754 | RubberDandelionOmics

Gene overview

LXL04_028754

Reference: OH-1004 Chr: Chr06 Coordinates: 61139156-61151679 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3285 bp · LXL04_028754|LXL04_028754|OH1004|cDNA

ATGTTAACCATCTTGAATCAAACCTCCAGGACTACGACAATGCCTCCTAAAGGAATGAGCCCGGCGGCTgttcaagctttggttgcggcgagtgtagccgaagccttagcagcctatgaggccaCTCGACGACAGAACCAGGGACAAAGTGGAGGAAGCGGAGGTAGCGGTggtagcggaggtagtggtggaaatggagatagcgggggaaacctcaggacttgtacctacaaagactttatggggtgcaagccgaagtc...

CDS

Download CDS FASTA

3285 bp · LXL04_028754|LXL04_028754|OH1004|CDS

ATGTTAACCATCTTGAATCAAACCTCCAGGACTACGACAATGCCTCCTAAAGGAATGAGCCCGGCGGCTGTTCAAGCTTTGGTTGCGGCGAGTGTAGCCGAAGCCTTAGCAGCCTATGAGGCCACTCGACGACAGAACCAGGGACAAAGTGGAGGAAGCGGAGGTAGCGGTGGTAGCGGAGGTAGTGGTGGAAATGGAGATAGCGGGGGAAACCTCAGGACTTGTACCTACAAAGACTTTATGGGGTGCAAGCCGAAGTC...

Protein

Download Protein FASTA

1094 aa · LXL04_028754|LXL04_028754|OH1004|PROTEIN

MLTILNQTSRTTTMPPKGMSPAAVQALVAASVAEALAAYEATRRQNQGQSGGSGGSGGSGGSGGNGDSGGNLRTCTYKDFMGCKPKSFSGIGGVIELTRWFEKTESVFAISSCPENCKVKYAVCTFEDGALTWWNGHVQTMGLPMLLKEYCPRGEIQKLEQEFWNLTMKGSDIQNYTTRFSELAVLCPGMVTPEFKKVERYVWGLAPHIQSHVTTADPATFESAKALVVRLTDEGIRQGTMKKGHTARFCKSPAVGPAQE...

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_028754`
TK1151 ID	TkA07G207660
OH-1004 ID	LXL04_028754
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	55.100
Protein coverage (%)	TK1151 98.551 / OH-1004 27.514 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_028754

Location Chr06:61139156-61151679 (+)

Description Similar to GAL1: Galactokinase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g06580`	Sugar-1-kinase with a very high substrate specificity for the alpha-anomeric configuration of D-galacose (D-Gal).	No verified direct reference in this release
`At3g03920`	Required for ribosome biogenesis.	No verified direct reference in this release
`At5g18180`	Required for ribosome biogenesis.	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_028754 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000454 snoRNA guided rRNA pseudouridine synthesis Biological Process

GO:0006012 galactose metabolic process Biological Process

GO:0046835 carbohydrate phosphorylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0031429 box H/ACA snoRNP complex Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0004335 galactokinase activity Molecular Function

KEGG gene cross-reference

ath:AT3G03920

ath:AT3G06580

ath:AT5G18180

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.

Cytoplasm0.667

Rank 1 · LXL04_028754 · OH-1004

Nucleus0.414

Rank 2 · LXL04_028754 · OH-1004

Mitochondrion0.090

Rank 3 · LXL04_028754 · OH-1004

Cell membrane0.072

Rank 4 · LXL04_028754 · OH-1004

Endoplasmic reticulum0.064

Rank 5 · LXL04_028754 · 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.

PF19259.5Ty3_capsid83-227 aa

PF03732.25PEG10_N-capsid85-140 aa

PF00098.29zf-CCHC268-284 aa

PF04410.21Gar1360-393 aa

PF19259.5Ty3_capsid700-846 aa

PF03732.25PEG10_N-capsid704-759 aa

PF00098.29zf-CCHC887-903 aa

PF04410.21Gar1970-1015 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028754	`PF19259.5`	Ty3_capsid	83	227	3.2e-12	47.0
LXL04_028754	`PF03732.25`	PEG10_N-capsid	85	140	5.2e-17	62.7
LXL04_028754	`PF00098.29`	zf-CCHC	268	284	4.9e-09	36.6
LXL04_028754	`PF04410.21`	Gar1	360	393	3.2e-21	75.6
LXL04_028754	`PF19259.5`	Ty3_capsid	700	846	3.2e-12	47.0
LXL04_028754	`PF03732.25`	PEG10_N-capsid	704	759	5.2e-17	62.7
LXL04_028754	`PF00098.29`	zf-CCHC	887	903	4.9e-09	36.6
LXL04_028754	`PF04410.21`	Gar1	970	1015	3.2e-21	75.6

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
`Q9SEE5`	Arabidopsis thaliana	Galactokinase	45.045%	Swiss-Prot	weak database homology
`Q8VZT0`	Arabidopsis thaliana	Putative H/ACA ribonucleoprotein complex subunit 1-like protein 1	67.347%	Swiss-Prot	weak database homology
`Q9FK53`	Arabidopsis thaliana	H/ACA ribonucleoprotein complex subunit 1-like protein 2	63.265%	Swiss-Prot	weak database homology

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