LXL04_009252 | RubberDandelionOmics

Gene overview

LXL04_009252

Reference: OH-1004 Chr: Chr02 Coordinates: 121331539-121333711 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1068 bp · LXL04_009252|LXL04_009252|OH1004|cDNA

ATGAAGCTCACCGTAAAGACTCTTAAAGGGAGCCACTTTGAAATTAGGGTTCAACCTTCCGATACTATTATGGCAGTCAAGAAAAACATCGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTACTGATCCACAATGGTAAGGTTCTGAAAGACGAAACTACATTATTAGATAACAAAGTCTCGGAGGAAGGTTTTCTTGTTGTCATGCTAAGCAAGCAGACTAAAAGTTCTACATCAAGTGGAACTAC...

CDS

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1068 bp · LXL04_009252|LXL04_009252|OH1004|CDS

ATGAAGCTCACCGTAAAGACTCTTAAAGGGAGCCACTTTGAAATTAGGGTTCAACCTTCCGATACTATTATGGCAGTCAAGAAAAACATCGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTACTGATCCACAATGGTAAGGTTCTGAAAGACGAAACTACATTATTAGATAACAAAGTCTCGGAGGAAGGTTTTCTTGTTGTCATGCTAAGCAAGCAGACTAAAAGTTCTACATCAAGTGGAACTAC...

Protein

Download Protein FASTA

355 aa · LXL04_009252|LXL04_009252|OH1004|PROTEIN

MKLTVKTLKGSHFEIRVQPSDTIMAVKKNIEDVQGKDNYPCGQQLLIHNGKVLKDETTLLDNKVSEEGFLVVMLSKQTKSSTSSGTTSTQPLSTTTPASNPTSTSSSIPATATVTAPVPAVSETYGEAGSNVVVTNNNVDQTVQHIMDIGGGSWDKETVTRALQAAFNNPERAIDYLYSGIPDTVEVAPPVTQLPTTQVPPLSGGPNSSPLNLFPQEMPSGGTGGNLGSLDFLRNNEQFQALRTMVQSNPQILQPMLQEL...

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_009252`
TK1151 ID	TkA03G412920
OH-1004 ID	LXL04_009252
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_009252

Location Chr02:121331539-121333711 (-)

Description Similar to RAD23B: Ubiquitin receptor RAD23b

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g79650`	May be involved in nucleotide excision repair (By similarity).	The RAD23 family provides an essential connection between the 26S proteasome and ubiquitylated proteins in Arabidopsis.2010 · DOI: 10.1105/tpc.109.072660 RAD4 and RAD23/HMR Contribute to Arabidopsis UV Tolerance.2017 · DOI: 10.3390/genes9010008
`At1g16190`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release
`At5g38470`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release
`At3g02540`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0407200`	May be involved in nucleotide excision repair (By similarity).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009252 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006289 nucleotide-excision repair Biological Process

GO:0009409 response to cold Biological Process

GO:0009411 response to UV Biological Process

GO:0009650 UV protection Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0003684 damaged DNA binding Molecular Function

GO:0031593 polyubiquitin modification-dependent protein binding Molecular Function

KEGG gene cross-reference

ath:AT1G16190

ath:AT1G79650

ath:AT3G02540

ath:AT5G38470

dosa:Os09g0407200

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.

Cytoplasm0.683

Rank 1 · LXL04_009252 · OH-1004

Nucleus0.636

Rank 2 · LXL04_009252 · OH-1004

Endoplasmic reticulum0.051

Rank 3 · LXL04_009252 · OH-1004

Cell membrane0.040

Rank 4 · LXL04_009252 · OH-1004

Mitochondrion0.035

Rank 5 · LXL04_009252 · 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.

PF00240.30ubiquitin3-76 aa

PF00627.38UBA141-177 aa

PF09280.17XPC-binding230-285 aa

PF00627.38UBA310-346 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009252	`PF00240.30`	ubiquitin	3	76	7.7e-15	55.1
LXL04_009252	`PF00627.38`	UBA	141	177	3.3e-21	75.4
LXL04_009252	`PF09280.17`	XPC-binding	230	285	1.2e-23	83.2
LXL04_009252	`PF00627.38`	UBA	310	346	3.3e-21	75.4

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
`Q84L33`	Arabidopsis thaliana	Ubiquitin receptor RAD23b	69.149%	Swiss-Prot	strong database homology
`Q84L32`	Arabidopsis thaliana	Probable ubiquitin receptor RAD23a	68.817%	Swiss-Prot	strong database homology
`Q84L30`	Arabidopsis thaliana	Ubiquitin receptor RAD23d	52.987%	Swiss-Prot	strong database homology
`Q84L31`	Arabidopsis thaliana	Ubiquitin receptor RAD23c	47.991%	Swiss-Prot	moderate database homology
`Q40742`	Oryza sativa subsp. japonica	Probable ubiquitin receptor RAD23	51.026%	Swiss-Prot	strong database homology

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