U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC4348965 DNA ligase 1 [ Oryza sativa Japonica Group (Japanese rice) ]

Gene ID: 4348965, updated on 10-Oct-2024

Summary

Go to the top of the page Help
Gene symbol
LOC4348965
Gene description
DNA ligase 1
Locus tag
OSNPB_100489200
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Oryza sativa Japonica Group
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC4348965 in Genome Data Viewer
Location:
chromosome: 10
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 10 NC_089044.1 (19221479..19228280, complement)
102 previous assembly IRGSP-1.0 (GCF_001433935.1) 10 NC_029265.1 (18552940..18559660, complement)

Chromosome 10 - NC_089044.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC136353646 Neighboring gene putative GEM-like protein 8 Neighboring gene probable protein arginine N-methyltransferase 6.2 Neighboring gene putative ripening-related protein 6 Neighboring gene putative ripening-related protein 7

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764
  2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
  3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

Go to the top of the page Help

Homology

Gene Ontology Provided by RefSeq

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 PubMed 
enables DNA ligase (ATP) activity IEA
Inferred from Electronic Annotation
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in DNA ligation IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
 PubMed 
involved_in lagging strand elongation IEA
Inferred from Electronic Annotation
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
DNA ligase 1
Names
Os10g0489200
NP_001410308.1
XP_015614474.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001423379.1 → NP_001410308.1  DNA ligase 1

    Status: VALIDATED

    Source sequence(s)
    AK120278, AP014966, CI421470

RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference ASM3414082v1 Primary Assembly

Genomic

  1. NC_089044.1 Reference ASM3414082v1 Primary Assembly

    Range
    19221479..19228280 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_015758988.3 → XP_015614474.1  DNA ligase 1 isoform X1

    UniProtKB/TrEMBL
    A0A0P0XW85, Q0IWT4
    Conserved Domains (1) summary
    PLN03113
    Location:170 → 905
    PLN03113; DNA ligase 1; Provisional
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials