Gene detail

Detailed information of evm.model.Ap9.1905 in Astrangia poculata

Genomic Location: Ap9:20818704...20842031
NR annotation: XP_022804578.1, DNA ligase 4-like isoform X1 [Stylophora pistillata]
Species Astrangia poculata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.Ap9.1905

atggcgggagtttcttcggctgaagtagcttcccaggtgccgttttatgatctgtgtttgttgttggagaagatagcagatacgccaggaactgaaaagaagaagaagattttgacaacattcgtcagttcttggagggaggctcatggaaagctacatggaactgctaaaacacctgactcattccattctgctatgcggctgttgctacctcaattggacaaagaaagaggagcttatggaataaaggaggttgtactggcaaaatattacatggaaatactgagtataggtaaagacactgctgatgggcgtaaactgttgaactatagagcacccaaacatgccaaacaggattcagtggctgattttgccagtgtggcttactttgttttgagaaacaggtgtcctgaaaagggcagtttaaagattgaccatgttaacaagcatcttgatcaagtggcacaggcaaatcttgaacgcaaacgagatgatgtcaagaaagctctacagcttcttctcaggaacacaagtgctcttgaacagaaatggttaatcaggatcattttcaaggaactaaagattggcctcagtgagaactctgtgtttaacgtttaccatcctgatgctcttgagctttacagtgtctgtaacagtttacccaaggtatgcttggatcttcatgatcgtagaatcaggatgaacgaggcagagatgactttgttctcgccattcagacccatgttggccgatagaggaagcattggagaggtagaaaagcttatggacaatcaatcattttacatagagacaaagatagatggagagagaatgcaagtccataaacagggagattctttcatgtatttttctagaagtgccaatgagtacactcatgtgtttggttctaactcatctactggagttctcacacctcatatcgcttgttgtttttcaagttctgtacattcttgcatactggatggagaaatgattgtgattgatcctgcaacagatgtatggatatccaaaggcatgaatgttgatgtgaaatctttaactacttatgaaaacggtcatcatccctgttttgttgtgtttgatatgcttgttattaatgagaaaaagcttgccaatgttcctctgagtgaaaggatcaaatccatggaaaaaacgctgaagccccagcctggctaccttcagtttgttgaaaggcacgatgcctcaacaaaggaagatgtagtaaaagctcttaatgatgcaattgacaaaagagaagagggcttggtcatcaaatcaccatcctctatatataaaccgaaccagagaagtggaagtggctgggtgaagatcaagccagaatatgttgatagtttaagcgatgagttggatctgctgattgttggtggctattttggagttggtcgccgtagcggcatgatatctcattttatgtgtgcagtggccgtgtcatccaacactccaggtgaacaccctaaagtgttccactcattttgcaaggtggggtccggttacacaatgaacgagctgcgtgaattagatcaacagttgcgtccacactggaatgtgtttgatactaaaaagcctcccacatctattattctggcacctggatacaaagaaaaaccagatgtgtggattgaaccatccaagtcaaagatagttcagatcaaggctacagaaattataacatccgacaagttcaaaactggtattactcttcgctttccaagactggaggctgttcgtaatgataagatgtggtatgaatgcttggacctaaatgagctggccaggctaaaatcggtggcagaaggaaagctgacgtaccagcacactagtgctgaggaaaaatctgaacctgccaagaaaaggcgacgggaagctgcaagaatcgagcatacgcgtactgtagcgcagcattttaaaccagctgatgtgtcatctgttaaagaagtatcacaaatgttccacgacaaggagttttatattgtcaatggtcctacgtcgcattccaaggctctactggagaagaaagttgctgagaatggaggcacgttcactcaaaaccctggccctgacacgttctgtatcgttgctgatagaatcaatgtgagggttaaaaacatcatcagccagaaacagttcgatgttgtgaaggcatcgtggcttataaactgcttggactgtggtgaagtgaagccgtggcttccaagtgacatgtttcactcgtcctcacggaccgctgataaatttgctgaggaatatgatcgccatggagacagctatacagagaatgcaacaagtgaatcactcaagaaagtgttccgtaatgtccaagaaaaaaactccgcagttccactatcaacagatgaaatactggaaatatcacaacgctattttcccgataattcacctctgggattattcaaacattgcagggtgtaccttgatcagttcactcgtattggggatagttcaacgcgaatacctaactgcagtttggagctagttggtttaaagcttcgcatgtatggcgcccaggtcactagcagtcttgacagcaaagtaacacatgttgtgattgacggaagtgaattttgccgatttgaagaacttcaaaaaataacccaagaaaggcatgcaaggcaacatcttgtcacgctagactgggtcacgcaatcagtggaagctgaaaaggtcttactagaaagacatttcagaccattattatga

Transcript

evm.model.Ap9.1905

ATGGCGGGAGTTTCTTCGGCTGAAGTAGCTTCCCAGGTGCCGTTTTATGATCTGTGTTTGTTGTTGGAGAAGATAGCAGATACGCCAGGAACTGAAAAGAAGAAGAAGATTTTGACAACATTCGTCAGTTCTTGGAGGGAGGCTCATGGAAAGCTACATGGAACTGCTAAAACACCTGACTCATTCCATTCTGCTATGCGGCTGTTGCTACCTCAATTGGACAAAGAAAGAGGAGCTTATGGAATAAAGGAGGTTGTACTGGCAAAATATTACATGGAAATACTGAGTATAGGTAAAGACACTGCTGATGGGCGTAAACTGTTGAACTATAGAGCACCCAAACATGCCAAACAGGATTCAGTGGCTGATTTTGCCAGTGTGGCTTACTTTGTTTTGAGAAACAGGTGTCCTGAAAAGGGCAGTTTAAAGATTGACCATGTTAACAAGCATCTTGATCAAGTGGCACAGGCAAATCTTGAACGCAAACGAGATGATGTCAAGAAAGCTCTACAGCTTCTTCTCAGGAACACAAGTGCTCTTGAACAGAAATGGTTAATCAGGATCATTTTCAAGGAACTAAAGATTGGCCTCAGTGAGAACTCTGTGTTTAACGTTTACCATCCTGATGCTCTTGAGCTTTACAGTGTCTGTAACAGTTTACCCAAGGTATGCTTGGATCTTCATGATCGTAGAATCAGGATGAACGAGGCAGAGATGACTTTGTTCTCGCCATTCAGACCCATGTTGGCCGATAGAGGAAGCATTGGAGAGGTAGAAAAGCTTATGGACAATCAATCATTTTACATAGAGACAAAGATAGATGGAGAGAGAATGCAAGTCCATAAACAGGGAGATTCTTTCATGTATTTTTCTAGAAGTGCCAATGAGTACACTCATGTGTTTGGTTCTAACTCATCTACTGGAGTTCTCACACCTCATATCGCTTGTTGTTTTTCAAGTTCTGTACATTCTTGCATACTGGATGGAGAAATGATTGTGATTGATCCTGCAACAGATGTATGGATATCCAAAGGCATGAATGTTGATGTGAAATCTTTAACTACTTATGAAAACGGTCATCATCCCTGTTTTGTTGTGTTTGATATGCTTGTTATTAATGAGAAAAAGCTTGCCAATGTTCCTCTGAGTGAAAGGATCAAATCCATGGAAAAAACGCTGAAGCCCCAGCCTGGCTACCTTCAGTTTGTTGAAAGGCACGATGCCTCAACAAAGGAAGATGTAGTAAAAGCTCTTAATGATGCAATTGACAAAAGAGAAGAGGGCTTGGTCATCAAATCACCATCCTCTATATATAAACCGAACCAGAGAAGTGGAAGTGGCTGGGTGAAGATCAAGCCAGAATATGTTGATAGTTTAAGCGATGAGTTGGATCTGCTGATTGTTGGTGGCTATTTTGGAGTTGGTCGCCGTAGCGGCATGATATCTCATTTTATGTGTGCAGTGGCCGTGTCATCCAACACTCCAGGTGAACACCCTAAAGTGTTCCACTCATTTTGCAAGGTGGGGTCCGGTTACACAATGAACGAGCTGCGTGAATTAGATCAACAGTTGCGTCCACACTGGAATGTGTTTGATACTAAAAAGCCTCCCACATCTATTATTCTGGCACCTGGATACAAAGAAAAACCAGATGTGTGGATTGAACCATCCAAGTCAAAGATAGTTCAGATCAAGGCTACAGAAATTATAACATCCGACAAGTTCAAAACTGGTATTACTCTTCGCTTTCCAAGACTGGAGGCTGTTCGTAATGATAAGATGTGGTATGAATGCTTGGACCTAAATGAGCTGGCCAGGCTAAAATCGGTGGCAGAAGGAAAGCTGACGTACCAGCACACTAGTGCTGAGGAAAAATCTGAACCTGCCAAGAAAAGGCGACGGGAAGCTGCAAGAATCGAGCATACGCGTACTGTAGCGCAGCATTTTAAACCAGCTGATGTGTCATCTGTTAAAGAAGTATCACAAATGTTCCACGACAAGGAGTTTTATATTGTCAATGGTCCTACGTCGCATTCCAAGGCTCTACTGGAGAAGAAAGTTGCTGAGAATGGAGGCACGTTCACTCAAAACCCTGGCCCTGACACGTTCTGTATCGTTGCTGATAGAATCAATGTGAGGGTTAAAAACATCATCAGCCAGAAACAGTTCGATGTTGTGAAGGCATCGTGGCTTATAAACTGCTTGGACTGTGGTGAAGTGAAGCCGTGGCTTCCAAGTGACATGTTTCACTCGTCCTCACGGACCGCTGATAAATTTGCTGAGGAATATGATCGCCATGGAGACAGCTATACAGAGAATGCAACAAGTGAATCACTCAAGAAAGTGTTCCGTAATGTCCAAGAAAAAAACTCCGCAGTTCCACTATCAACAGATGAAATACTGGAAATATCACAACGCTATTTTCCCGATAATTCACCTCTGGGATTATTCAAACATTGCAGGGTGTACCTTGATCAGTTCACTCGTATTGGGGATAGTTCAACGCGAATACCTAACTGCAGTTTGGAGCTAGTTGGTTTAAAGCTTCGCATGTATGGCGCCCAGGTCACTAGCAGTCTTGACAGCAAAGTAACACATGTTGTGATTGACGGAAGTGAATTTTGCCGATTTGAAGAACTTCAAAAAATAACCCAAGAAAGGCATGCAAGGCAACATCTTGTCACGCTAGACTGGGTCACGCAATCAGTGGAAGCTGAAAAGGTCTTACTAGAAAGACATTTCAGACCATTATTATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q90YB1	DNA ligase 4 OS=Gallus gallus OX=9031 GN=LIG4 PE=2 SV=2
Q8BTF7	DNA ligase 4 OS=Mus musculus OX=10090 GN=Lig4 PE=2 SV=2
G3GTP0	DNA ligase 4 OS=Cricetulus griseus OX=10029 GN=LIG4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002928 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04679 all species →	DNA_ligase_A_C	ATP dependent DNA ligase C terminal region	Family	Interproscan
PF00533 all species →	BRCT	BRCA1 C Terminus (BRCT) domain	Family	Interproscan
PF01068 all species →	DNA_ligase_A_M	ATP dependent DNA ligase domain	Domain	Interproscan
PF11411 all species →	DNA_ligase_IV	DNA ligase IV	Family	Interproscan
PF04675 all species →	DNA_ligase_A_N	DNA ligase N terminus	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR029710 all species →	Family	DNA ligase 4	Interproscan
IPR044125 all species →	Domain	DNA Ligase 4, adenylation domain	Interproscan
IPR000977 all species →	Family	DNA ligase, ATP-dependent	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR021536 all species →	Domain	DNA ligase IV domain	Interproscan
IPR036599 all species →	Homologous_superfamily	DNA ligase, ATP-dependent, N-terminal domain superfamily	Interproscan
IPR012308 all species →	Domain	DNA ligase, ATP-dependent, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45997 all species →	DNA LIGASE 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005958 all species →	Cellular Component	DNA-dependent protein kinase-DNA ligase 4 complex	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0032807 all species →	Cellular Component	DNA ligase IV complex	Interproscan
GO:0051103 all species →	Biological Process	DNA ligation involved in DNA repair	Interproscan
GO:0071897 all species →	Biological Process	DNA biosynthetic process	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10777	LIG4, DNL4; DNA ligase 4	EC:6.5.1.1	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.