Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Pathway
Basic Information
Gene ID
AmTr_scaff00064.85.v1.0.g
View in Genome Browser
Position
AmTr_scaff00064:3346701-3347389 (-)
688bp
Gene Type
gene
Gene Description (Protein Product)
DNA ligase (ATP) activity
Organism
Amborella trichopoda
Also AS AT1G08130AMTR_s00064p00190330

Gene Structure

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Domain
Database EntryID E-Value Start end InterPro ID Description

Regulation&Interaction
Protein-protein interaction (PPI)
AmTr_scaff00075.19.v1.0.g polynucleotide
AmTr_scaff00066.271.v1.0.g May play an essential role at the early stage of chromosomal DNA replication by coupling the polymerase alpha primase complex to the cellular replication machinery
AmTr_scaff00156.38.v1.0.g ubiquitin receptor
Regulatory gene
AmTr_scaff00006.141.v1.0.g dof zinc finger protein
AmTr_scaff00010.496.v1.0.g Cyclic dof factor
AmTr_scaff00012.109.v1.0.g dof zinc finger protein

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Annotation

Orthologous Group
Orthologous ID Species Number All hits in PereRegDB Hits of this species Orthologous Detail


Pathway
Go Pathway KEGG Pathway
GO Term Description GO Category
GO:0000012 single strand break repair BP
GO:0000228 nuclear chromosome CC
GO:0000278 mitotic cell cycle BP
GO:0000302 response to reactive oxygen species BP
GO:0000726 obsolete non-recombinational repair BP
GO:0003674 molecular_function MF
GO:0003676 nucleic acid binding MF
GO:0003677 DNA binding MF
GO:0003824 catalytic activity MF
GO:0003909 DNA ligase activity MF
GO:0003910 DNA ligase (ATP) activity MF
GO:0005488 binding MF
GO:0005575 cellular_component CC
GO:0005622 intracellular anatomical structure CC
GO:0005623 obsolete cell CC
GO:0005634 nucleus CC
GO:0005654 nucleoplasm CC
GO:0005657 replication fork CC
GO:0005694 chromosome CC
GO:0005730 nucleolus CC
GO:0005737 cytoplasm CC
GO:0005739 mitochondrion CC
GO:0006139 nucleobase-containing compound metabolic process BP
GO:0006259 DNA metabolic process BP
GO:0006260 DNA replication BP
GO:0006261 DNA-templated DNA replication BP
GO:0006266 DNA ligation BP
GO:0006271 DNA strand elongation involved in DNA replication BP
GO:0006273 lagging strand elongation BP
GO:0006281 DNA repair BP
GO:0006283 transcription-coupled nucleotide-excision repair BP
GO:0006284 base-excision repair BP
GO:0006289 nucleotide-excision repair BP
GO:0006297 nucleotide-excision repair, DNA gap filling BP
GO:0006298 mismatch repair BP
GO:0006302 double-strand break repair BP
GO:0006303 double-strand break repair via nonhomologous end joining BP
GO:0006304 DNA modification BP
GO:0006310 DNA recombination BP
GO:0006725 cellular aromatic compound metabolic process BP
GO:0006807 nitrogen compound metabolic process BP
GO:0006950 response to stress BP
GO:0006974 cellular response to DNA damage stimulus BP
GO:0006979 response to oxidative stress BP
GO:0006996 organelle organization BP
GO:0007049 cell cycle BP
GO:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0009058 biosynthetic process BP
GO:0009059 macromolecule biosynthetic process BP
GO:0009636 response to toxic substance BP
GO:0009653 anatomical structure morphogenesis BP
GO:0009987 cellular process BP
GO:0010035 response to inorganic substance BP
GO:0016043 cellular component organization BP
GO:0016070 RNA metabolic process BP
GO:0016874 ligase activity MF
GO:0016886 ligase activity, forming phosphoric ester bonds MF
GO:0022402 cell cycle process BP
GO:0022616 DNA strand elongation BP
GO:0031974 membrane-enclosed lumen CC
GO:0031981 nuclear lumen CC
GO:0032502 developmental process BP
GO:0033260 nuclear DNA replication BP
GO:0033554 cellular response to stress BP
GO:0033567 DNA replication, Okazaki fragment processing BP
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0034645 cellular macromolecule biosynthetic process BP
GO:0035510 DNA dealkylation BP
GO:0035753 maintenance of DNA trinucleotide repeats BP
GO:0042221 response to chemical BP
GO:0042493 response to xenobiotic stimulus BP
GO:0042542 response to hydrogen peroxide BP
GO:0043170 macromolecule metabolic process BP
GO:0043226 organelle CC
GO:0043227 membrane-bounded organelle CC
GO:0043228 non-membrane-bounded organelle CC
GO:0043229 intracellular organelle CC
GO:0043231 intracellular membrane-bounded organelle CC
GO:0043232 intracellular non-membrane-bounded organelle CC
GO:0043233 organelle lumen CC
GO:0043412 macromolecule modification BP
GO:0043570 maintenance of DNA repeat elements BP
GO:0043596 nuclear replication fork CC
GO:0044237 cellular metabolic process BP
GO:0044238 primary metabolic process BP
GO:0044249 cellular biosynthetic process BP
GO:0044260 cellular macromolecule metabolic process BP
GO:0044422 obsolete organelle part CC
GO:0044424 obsolete intracellular part CC
GO:0044427 obsolete chromosomal part CC
GO:0044428 obsolete nuclear part CC
GO:0044444 obsolete cytoplasmic part CC
GO:0044446 obsolete intracellular organelle part CC
GO:0044454 obsolete nuclear chromosome part CC
GO:0044464 obsolete cell part CC
GO:0044728 obsolete DNA methylation or demethylation BP
GO:0044786 cell cycle DNA replication BP
GO:0046483 heterocycle metabolic process BP
GO:0046677 response to antibiotic BP
GO:0048856 anatomical structure development BP
GO:0050896 response to stimulus BP
GO:0051103 DNA ligation involved in DNA repair BP
GO:0051276 chromosome organization BP
GO:0051716 cellular response to stimulus BP
GO:0070013 intracellular organelle lumen CC
GO:0070988 demethylation BP
GO:0071704 organic substance metabolic process BP
GO:0071840 cellular component organization or biogenesis BP
GO:0080111 DNA demethylation BP
GO:0090304 nucleic acid metabolic process BP
GO:0097159 organic cyclic compound binding MF
GO:0140097 catalytic activity, acting on DNA MF
GO:1901360 organic cyclic compound metabolic process BP
GO:1901363 heterocyclic compound binding MF
GO:1901576 organic substance biosynthetic process BP
GO:1901700 response to oxygen-containing compound BP
GO:1902969 mitotic DNA replication BP
GO:1903047 mitotic cell cycle process BP
GO:1903461 Okazaki fragment processing involved in mitotic DNA replication BP
KEGG Term Name Description
map03430 Mismatch repair DNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication, thereby preventing mutations from becoming permanent in dividing cells. MMR also suppresses homologous recombination and was recently shown to play a role in DNA damage signaling. Defects in MMR are associated with genome-wide instability, predisposition to certain types of cancer including HNPCC, resistance to certain chemotherapeutic agents, and abnormalities in meiosis and sterility in mammalian systems.
map03420 Nucleotide excision repair Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the NER pathway are linked to at least three diseases: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The repair of damaged DNA involves at least 30 polypeptides within two different sub-pathways of NER known as transcription-coupled repair (TCR-NER) and global genome repair (GGR-NER). TCR refers to the expedited repair of lesions located in the actively transcribed strand of genes by RNA polymerase II (RNAP II). In GGR-NER the first step of damage recognition involves XPC-hHR23B complex together with XPE complex (in prokaryotes, uvrAB complex). The following steps of GGR-NER and TCR-NER are similar.
map03410 Base excision repair Base excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair initiated by lesion-specific DNA glycosylases and completed by either of the two sub-pathways: short-patch BER where only one nucleotide is replaced and long-patch BER where 2-13 nucleotides are replaced. Each sub-pathway of BER relies on the formation of protein complexes that assemble at the site of the DNA lesion and facilitate repair in a coordinated fashion. This process of complex formation appears to provide an increase in specificity and efficiency to the BER pathway, thereby facilitating the maintenance of genome integrity by preventing the accumulation of highly toxic repair intermediates.
map03030 DNA replication A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (DnaB or MCM complex) precedes the DNA synthetic machinery and unwinds the duplex parental DNA in cooperation with the SSB or RPA. On the leading strand, replication occurs continuously in a 5 to 3 direction, whereas on the lagging strand, DNA replication occurs discontinuously by synthesis and joining of short Okazaki fragments. In prokaryotes, the leading strand replication apparatus consists of a DNA polymerase (pol III core), a sliding clamp (beta), and a clamp loader (gamma delta complex). The DNA primase (DnaG) is needed to form RNA primers. Normally, during replication of the lagging-strand DNA template, an RNA primer is removed either by an RNase H or by the 5 to 3 exonuclease activity of DNA pol I, and the DNA ligase joins the Okazaki fragments. In eukaryotes, three DNA polymerases (alpha, delta, and epsilon) have been identified. DNA primase forms a permanent complex with DNA polymerase alpha. PCNA and RFC function as a clamp and a clamp loader. FEN 1 and RNase H1 remove the RNA from the Okazaki fragments and DNA ligase I joins the DNA.