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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_017960
Reference: OH-1004 Chr: Chr04 Coordinates: 4299634-4306177 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3644 bp · LXL04_017960|LXL04_017960|OH1004|cDNA

GCATAAACACATAGTTTACACACACACAAAACCCTTTCCGATCAAAAATGTCAGTGGAGACGAAATTCAGCGTGATGTGCAGTCTATTCAACTGGATTCAGAAGTCAAAGTCTTCAACAAAAAAACGATCCAAGTTTCGGAAATTCCTCGACACGTATTGTAAACCCACGGATTACTTCGCTGCTGTCAGATTAATCCTCCCCAACCTCGACAGAGAGCGAGGATCTTACGGTTTGAAGGAGTCGGTGCTCGCCACTTGT...

CDS

Download CDS FASTA

3597 bp · LXL04_017960|LXL04_017960|OH1004|CDS

ATGTCAGTGGAGACGAAATTCAGCGTGATGTGCAGTCTATTCAACTGGATTCAGAAGTCAAAGTCTTCAACAAAAAAACGATCCAAGTTTCGGAAATTCCTCGACACGTATTGTAAACCCACGGATTACTTCGCTGCTGTCAGATTAATCCTCCCCAACCTCGACAGAGAGCGAGGATCTTACGGTTTGAAGGAGTCGGTGCTCGCCACTTGTATCATCGACGCCCTCGGAATGTCCAGAGAATCTCCCGACGCTCTTCG...

Protein

Download Protein FASTA

1198 aa · LXL04_017960|LXL04_017960|OH1004|PROTEIN

MSVETKFSVMCSLFNWIQKSKSSTKKRSKFRKFLDTYCKPTDYFAAVRLILPNLDRERGSYGLKESVLATCIIDALGMSRESPDALRLINWRKGGAKTGVNVGNFSLVASEVLQRRQGMISGGLTIKELNDLLDRLASSENRTEKTSILADLIKKTNAQEMKWIVMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCERLRDRNQRHKRQDIEVGKAVRPQLALRVANAASAWKKLQGKEVVIECKFDGDRIQI...

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.

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ID Mapping

Input IDLXL04_017960
Source versionOH-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 IDLXL04_017960
LocationChr04:4299634-4306177 (+)
DescriptionSimilar to LIG4: DNA ligase 4
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g57160 DNA ligase involved in DNA non-homologous end joining (NHEJ).
The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA.2003 · DOI: 10.1093/nar/gkg458

Rice

Reference gene IDPossible functionPapers / DOI
Os04g0606450 DNA ligase involved in DNA non-homologous end joining (NHEJ); required for double-strand break (DSB) repair. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_017960 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000012 single strand break repair Biological Process
GO:0006284 base-excision repair Biological Process
GO:0006297 nucleotide-excision repair, DNA gap filling Biological Process
GO:0006302 double-strand break repair Biological Process
GO:0006303 double-strand break repair via nonhomologous end joining Biological Process
GO:0006310 DNA recombination Biological Process
GO:0006974 DNA damage response Biological Process
GO:0008283 cell population proliferation Biological Process
GO:0010165 response to X-ray Biological Process
GO:0010212 response to ionizing radiation Biological Process
GO:0010332 response to gamma radiation Biological Process
GO:0035019 somatic stem cell population maintenance Biological Process
KEGG gene cross-reference
ath:AT5G57160
hsa:3981
pon:100173511
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.

Nucleus0.934
Rank 1 · LXL04_017960 · OH-1004
Cytoplasm0.141
Rank 2 · LXL04_017960 · OH-1004
Mitochondrion0.026
Rank 3 · LXL04_017960 · OH-1004
Cell membrane0.025
Rank 4 · LXL04_017960 · OH-1004
Endoplasmic reticulum0.011
Rank 5 · LXL04_017960 · 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.

PF04675.20DNA_ligase_A_N6-186 aa
PF01068.27DNA_ligase_A_M226-441 aa
PF04679.22DNA_ligase_A_C465-584 aa
PF00533.34BRCT654-725 aa
PF16589.13BRCT_2655-735 aa
PF12738.14PTCB-BRCT669-714 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_017960PF04675.20DNA_ligase_A_N61864.1e-40138.5
LXL04_017960PF01068.27DNA_ligase_A_M2264416.5e-43147.5
LXL04_017960PF04679.22DNA_ligase_A_C4655841.4e-1248.6
LXL04_017960PF00533.34BRCT6547254.1e-1350.0
LXL04_017960PF16589.13BRCT_26557352.5e-1866.9
LXL04_017960PF12738.14PTCB-BRCT6697145e-1040.0

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.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9LL84Arabidopsis thalianaDNA ligase 459.311%Swiss-Protstrong database homology
Q7X7E9Oryza sativa subsp. japonicaPutative DNA ligase 461.517%Swiss-Protmoderate database homology

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