LXL04_014043 | RubberDandelionOmics

Gene overview

LXL04_014043

Reference: OH-1004 Chr: Chr03 Coordinates: 41079089-41088546 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3639 bp · LXL04_014043|LXL04_014043|OH1004|cDNA

ATGCAGGCAGAAAAACGATTATATAGCGATGAGCAAGACAGCCGTTTGTATAATATGGCTATAGTGATGGGGAATTGCAGATTACAGCCTCGACACATCCATTTGGGGATCGAATTAGGGCTTGGGTGGAAAAGCGACAAGGAAAAATATCGAAGACTTCGACGAGGACAATTCCGAGAAGGGGGTCGTTGTGGAAGTGGTTTTCGCTATCGTCGTCCTGTCGGATGTGATTGTAAGGATCCGAAACCTCCAATGGAAAG...

CDS

Download CDS FASTA

3639 bp · LXL04_014043|LXL04_014043|OH1004|CDS

ATGCAGGCAGAAAAACGATTATATAGCGATGAGCAAGACAGCCGTTTGTATAATATGGCTATAGTGATGGGGAATTGCAGATTACAGCCTCGACACATCCATTTGGGGATCGAATTAGGGCTTGGGTGGAAAAGCGACAAGGAAAAATATCGAAGACTTCGACGAGGACAATTCCGAGAAGGGGGTCGTTGTGGAAGTGGTTTTCGCTATCGTCGTCCTGTCGGATGTGATTGTAAGGATCCGAAACCTCCAATGGAAAG...

Protein

Download Protein FASTA

1212 aa · LXL04_014043|LXL04_014043|OH1004|PROTEIN

MQAEKRLYSDEQDSRLYNMAIVMGNCRLQPRHIHLGIELGLGWKSDKEKYRRLRRGQFREGGRCGSGFRYRRPVGCDCKDPKPPMERVSWSDSNPGRRFFNCVDSLIGDDTKKCDFFQWFDPELPNEHYLNWVNKIKNELKSFKDKSYCGKLIKKVAELEKMNEDLQVQIVAEREANEGARVQAAEERAKLVKEMQVLKKKVQVVVGLLVFAVGVMLVFEVFEVEGSWYMKLTFGDICAQAVGLLGTNCIEYAGLYDASD...

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_014043`
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_014043

Location Chr03:41079089-41088546 (-)

Description Similar to RAD4: DNA repair protein RAD4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g16630`	Essential protein.	CENTRIN2 interacts with the Arabidopsis homolog of the human XPC protein (AtRAD4) and contributes to efficient synthesis-dependent repair of bulky DNA lesions.2006 · DOI: 10.1007/s11103-006-0016-9 RAD4 and RAD23/HMR Contribute to Arabidopsis UV Tolerance.2017 · DOI: 10.3390/genes9010008

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_014043 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000720 pyrimidine dimer repair by nucleotide-excision repair Biological Process

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0006281 DNA repair Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0006298 mismatch repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006974 DNA damage response Biological Process

GO:0009410 response to xenobiotic stimulus Biological Process

GO:0009411 response to UV Biological Process

GO:0009650 UV protection Biological Process

GO:0010224 response to UV-B Biological Process

GO:0010777 meiotic mismatch repair involved in reciprocal meiotic recombination Biological Process

KEGG gene cross-reference

ath:AT5G16630

dme:Dmel_CG8153

hsa:7508

mmu:22591

spo:2542967

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.

Nucleus0.948

Rank 1 · LXL04_014043 · OH-1004

Cytoplasm0.083

Rank 2 · LXL04_014043 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_014043 · OH-1004

Plastid0.019

Rank 4 · LXL04_014043 · OH-1004

Endoplasmic reticulum0.017

Rank 5 · LXL04_014043 · 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.

PF03835.22Rad4777-884 aa

PF10403.15BHD_1898-947 aa

PF10404.15BHD_2951-1013 aa

PF10405.16BHD_31020-1092 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014043	`PF03835.22`	Rad4	777	884	2.1e-21	76.9
LXL04_014043	`PF10403.15`	BHD_1	898	947	3.4e-17	62.8
LXL04_014043	`PF10404.15`	BHD_2	951	1013	1.4e-13	52.0
LXL04_014043	`PF10405.16`	BHD_3	1020	1092	6.7e-25	88.0

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
`Q8W489`	Arabidopsis thaliana	DNA repair protein RAD4	47.953%	Swiss-Prot	moderate database homology

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