XLOC_030541 (lig3)


Basic Information

Item Value
gene id XLOC_030541
gene name lig3
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007116.7
NCBI id CM002889.2
chromosome length 72500376
location 60847823 ~ 60873092 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00059625
GCACTGAACAGGAACCACTTCCAAACAAAGAGGAAGAACTCGTGTGATTTAAAGGGGACAGCACACAATACAGAAATCATGCTCTTTTGCTAATACATCTGtgagtgctttttaaaaatgaaatccgGAGCTTGGGATCGGCTAACAATGAAGACTGAGGATTCGCGTCTATTTTATGAGATGAAGACTTTTCTGTCTTACTGAACTTTATGCCCAGTCTTTGGCTTGGCAGGGCATTAAGAACACTCAGCAGATCATCTTTGACCAAAATTTCTTGGGAGCCTTTATTTAGAGCAACACTCAAACACCAATATCTCCAGTGCTCGAGGACTCTTATATTTACACGGGGCTCTGAATCAAGCCCCAGTGGAGTCTTTTTCTGTGCGCCACACACTCCAGCATTTACTTTAATATCCAGCTCTTATTTCCACATTTCCTGGCCTGTGCGGAGGAGTGAACAAGCGGATATGGCGGAGCAGAGATACTGTGTTGAATATGCCAAACGTGGCACGGCTGGCTGCAAGAAATGCAAAGACAAGATCATGAAAGGTCTGGTCAGGATCGGCAAGATCGTTCCAAACCCATTCAGCGAGTCTGCAGGGGAAATGAAGGAATGGTATCATGTAAAGTGTATCTTTGAGAAGCTTGAGAGAGCGCGGGCCACCACAAAGAAGATTGAGGACATCACTGAACTGGAGGGATGGGAGGAACTTCAGGATGAGGATAAAGATCTCATCAATAAACACGTTTCAGAACTGGCAGCTAAAGTTAATTCAACCCCAAAGAAGAAAGTGCAAGCAAAGCTAAACACCAGTGGGCAGCTGTCATCGCCGCCAGCTGATCCAACAGTCAATGCTCCTCGCAAGTTTTCTGGCTTCACAGCTACCAAGGCCGGTTCCTCTTCCTCCAGTCCTGGACCATCTCCAGCCAAACCCGCTCAGGGTAGCGTTTTATCAGCTCAGATGTGTGACCCCACACATAAAGACAACTTACTTCGTGAGTTCAGAAAACTCTGTGCTTTAGTGGCAGAGAAGTCGGGCTACAACGCCAAGACGGAGATCGTCAGAGACTTCTTAACAAAAGGCTCAGGTGGAGACAAATTCAGAGGAGATTTGTACCTGACAGTGAAGCTTCTCCTCCCAGGCGTAGTGAAGAATGTGTACAACCTCAATGACAAACAAATCGTCAAGCTTTTTAGCCGCATACTGAATTGCAATCAGGATGACATGGTGCAAGACTTGGAACAGGGAGATGTTTCGGAGACGGTGCGGATGTTTTTCGAGGAAAGCAAGTCTTTCCCTCCTTCAGCAAAAAGTCTTCTGACCATCCAAGAGGTGGATGCTTCGCTGAGCCGATTATCCCAGCTCACAAAGGAGGACGATCAGCAGGCAGAGCTGCAGAGCATTGCCAAAAAATGCACCGGGAATGATCTGAAGTGCTACATTCGTTTGGTCAAACATGATTTGAAAATCAACTCAGGGGCGAAACACATTTTGGATGCTGTAGACCCCAATGCCTATGATGCCTTCAAAGCCTCCCGTAATCTCGGTGATGTGATAGACAGAGTGCTGCGTAACCAGCAGGATGCTTCTAATGGAACTGGCCCCCGAAAGATCCTCAGCATCGAGGCATCTCTGATGACTCCAGTACAGCCAATGCTGGCAGAGGCATGCAAGTCCATTGAGTACGCCATGAAGAAGTGTCCTAATGGGATGTATTCTGAGATCAAATATGATGGTGAGCGCGTGCAGGTCCATAAGAACGGCAATCACTTCAGTTACTTCAGTCGCAGTCTCAAACCAGTCCTCCCACACAAGGTTGCCCATTTTAAGGACTTCATACCGCAGGCGTTTGCTGGTGGTCATAGCATGATCCTTGATGCTGAAGTTCTTCTTATTGACACAAAGACTAGCAAACCACTGCCTTTTGGGACTCTTGGAGTACACAAGAAAGCCGCTTTTCAGGATGCTCAAGTGGGCCTGTTCGTGTTCGActgcatttattttaatggtgTCAGTCTAATGGACAAGCCTCTCTGTGAGAGAAGAAAGTTTCTCCATGATAATATGGTGGAAGTTCCTAACCGAATTCTGTTCTCAGAAATGAAGCATGTCACAAGAGCTCCTGATCTGGCAGAAATGATCACGCGTGTCATCAGAGAGGGGCTGGAGGGCTTGGTTCTGAAGGATATAAAGGGCCTTTATGAACCAGGAAAACGCCACTGGCTGAAGGTGAAGAAAGACTATCTGAATGAAGGAGCGATGGCGGACACTGCTGATCTTGTGGTGCTTGGAGCCTTCTATGGCAAAGGCTCAAATGGTGGAATTATGTCCAGTTTCCTCATGGGCTGCTATGACCCGGAATCCAGGAAGTGGTGCACCGTTACCAAGTGTTCAGGAGGCTTCGACGACGCCATGTTAGACAGACTGCAGAAAGATTTGGACGTGATTAAAATTGGCAAGGATCCAAGCAAGATCCCAGGATGGTTGAAGATTGTCAAGAACTATTACCCAGATTTCATTATCCGAGATCCACAAAAAGCACCAGTGTGGGAAATCACAGGAGCAGAGTTTTCTAAATCTGAAATGCACACTGCTGATGGCATATCCATCCGATTCCCACGATGCACCCGAATGCGTGATGACAAGGACTGGAAGACGGCAACTAACCTTCAGCAGCTCAAGgaGCTATATCGCATCTCAAAGGAGAATTGTGATTTTGAGGTGACCGCTGGTCCATCCAAAGCGAACCAAAATGACAAGAGCTCCTCAGGAGGTGAGAGCGGAGGAAGCTCTCCATCTGCATCTCGCGGAGCATCCACAGCTAACAAACCCAAAAATGGTCATACCCCCAAAGCAAAGGCTGCGAAAACAGAATCATCTGCTCCGGCAGTTAAGAGGAAACTACCAGCTGAGAAACAAGATGTTAAGAAGATAAAAACAGAATCGGTTCACAGCAATGGTCAAAGCAAATTGAAGAGCGTTCCAACAACCGACCCGAAGCAAGAAAAGACACTACTTGACATTTTCACCGGAGTAAAGCTCTACCTCCCTGAATCAGTGAAAGACTTTGAGAAGCTCCGACGCTACTTTCTAGCATACGATGGAGATTTGGTGCCCGAGTATGACTCTGCTTTAGCCACACACACGCTAGGACAGCCAGAGGATGGCAGTTCAGCCCAGAAGGTCACCTCCAACTGGATCTGGGAATGCATCCGGAAAAGGAGGGTGGTTCCCCCCTGCTGAACAAACCACACAAAGAGACATGCTGGAAGGACACTAGCACAAAGCTCAGGTTTGCTGTTCTCTAACAAGCAACGCCAATATATGAAAGACCCCTATAGCTTCTGCAATAGCGTTGTCACTCATGACAGACCGTGTTGAATGAACTTTTTCAAAAGTTAGCTTCTGAATAATTTTGTGTTGGATTTACCGCATTGTGGTATTCATTTCTTATGCTTTTCAATTGTTGCTTTCGACATGGCTGCATTTCTCACGATGgattttcatatttatgattTTAACCGTTTTGGTGTCATTTATTGACTAGTGCTGCCATATTCGTCACTAAAGTCAATAAGCGTAATGATTTCATGATGCTagtgtcatttatttgttttgatgAGGATTGGGTGTGTGGAGTGTGCTCTTGGGCGCAGGACGAGTGATTAACAATACGATAGTAACAGCCATGATTGCGAAATGAATAATTGTGTAGAGTAAATTGGGTAAGAGCCCTCGTGCTTAGTAATGGTAGTTGTGTGTAATTTCAGCTGTTCCTgttattacaattaaaacaaGCCTTTTTATGCACAAAGATGTTGATTTGTGCCTGAATGACGTCTGTTGAGCACGCAACAGGGAACCTTATTTCCAGAGTGATTATATGAGTGTCTGTATAACACAACATTAATTTtcatcatagttttttttttctttgtctaatCAGCAAGCTGCATTTTTAGACTTATACTGACACATAGAGGTGAGATTGAGCATAAAGCAAACAttgttttacactgaaaataatggTCAGATGgtgctttttttctgtttgtactgaggaagacctttttttttttctttttcatgtagGAAATTTTAAGGTGCCAACATTATGTAagagattttaataaaaaaaaaatgcaaagca

Function

symbol description
lig3 Predicted to enable DNA ligase (ATP) activity. Acts upstream of or within double-strand break repair via alternative nonhomologous end joining. Predicted to be located in nucleus. Predicted to be part of DNA ligase III-XRCC1 complex. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human LIG3 (DNA ligase 3).

GO:

id name namespace
GO:0006310 DNA recombination biological_process
GO:0006974 cellular response to DNA damage stimulus biological_process
GO:0071897 DNA biosynthetic process biological_process
GO:0097681 double-strand break repair via alternative nonhomologous end joining biological_process
GO:0043504 mitochondrial DNA repair biological_process
GO:0006260 DNA replication biological_process
GO:0006266 DNA ligation biological_process
GO:0006273 lagging strand elongation biological_process
GO:0006281 DNA repair biological_process
GO:0051103 DNA ligation involved in DNA repair biological_process
GO:0006288 base-excision repair, DNA ligation biological_process
GO:0070421 DNA ligase III-XRCC1 complex cellular_component
GO:0005737 cytoplasm cellular_component
GO:0003909 DNA ligase activity molecular_function
GO:0003910 DNA ligase (ATP) activity molecular_function
GO:0005524 ATP binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0000166 nucleotide binding molecular_function
GO:0008270 zinc ion binding molecular_function
GO:0016874 ligase activity molecular_function

KEGG:

id description
ko03410 Base excision repair
ko03400 DNA repair and recombination proteins

ZFIN:

id description
ZDB-GENE-030131-8453 Predicted to enable DNA ligase (ATP) activity. Acts upstream of or within double-strand break repair via alternative nonhomologous end joining. Predicted to be located in nucleus. Predicted to be part of DNA ligase III-XRCC1 complex. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human LIG3 (DNA ligase 3).

Ensembl:

ensembl_id ENSDARG00000052553

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00059625 True 4152 mRNA 0.45 21 60847823 60873092

Neighbor

gene id symbol gene type direction distance location
XLOC_030539 NA coding upstream 70300 60763937 ~ 60777523 (+)
XLOC_030540 CABZ01101667.1 coding upstream 71825 60775881 ~ 60775998 (+)
XLOC_030538 NA coding upstream 134083 60702425 ~ 60713740 (+)
XLOC_030537 tmem132e coding upstream 160204 60518611 ~ 60687619 (+)
XLOC_030536 NA coding upstream 621350 60225573 ~ 60226473 (+)
XLOC_030542 tmem248 coding downstream 13011 60886103 ~ 60906496 (+)
XLOC_030543 doc2b coding downstream 46286 60919378 ~ 61329656 (+)
XLOC_030544 CR932980.2 coding downstream 386860 61259952 ~ 61260067 (+)
XLOC_030545 NA coding downstream 476641 61349733 ~ 61354529 (+)
XLOC_030546 castor2 coding downstream 488723 61361815 ~ 61403813 (+)
XLOC_030533 NA non-coding upstream 625683 59605706 ~ 60222140 (+)
XLOC_030552 NA non-coding downstream 706354 61579446 ~ 61581273 (+)
XLOC_030553 NA non-coding downstream 706861 61579953 ~ 61580768 (+)
XLOC_030554 NA non-coding downstream 715516 61588608 ~ 61601237 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000059_04144039_04155667 LIG3 coding CI01000059 null 4143568 ~ 4155667 (+)