LIG1 (DNA ligase 1)

Gene

• Entrez ID: 3978
• Gene name: DNA ligase 1
• Gene symbol: LIG1
• Synonyms (NCBI Gene): IMD96, LIGI, hLig1
• Disease Acronyms (UniProt): IMD96
• Chromosome: 19
• Chromosome location: 19q13.33
• Summary: This gene encodes a member of the ATP-dependent DNA ligase protein family. The encoded protein functions in DNA replication, recombination, and the base excision repair process. Mutations in this gene that lead to DNA ligase I deficiency result in immunod

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT030288	hsa-miR-26b-5p	Microarray	19088304
MIRT045653	hsa-miR-149-5p	CLASH	23622248
MIRT040334	hsa-miR-615-3p	CLASH	23622248
MIRT2030323	hsa-miR-3064-3p	CLIP-seq
MIRT2030324	hsa-miR-4639-5p	CLIP-seq
MIRT2030325	hsa-miR-922	CLIP-seq
MIRT2261053	hsa-miR-1203	CLIP-seq
MIRT2261054	hsa-miR-342-3p	CLIP-seq
MIRT2261055	hsa-miR-4640-3p	CLIP-seq
MIRT2390142	hsa-miR-329	CLIP-seq
MIRT2261054	hsa-miR-342-3p	CLIP-seq
MIRT2390143	hsa-miR-362-3p	CLIP-seq
MIRT2390144	hsa-miR-377	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IEA
GO:0003909	Function	DNA ligase activity	IDA	9809069
GO:0003909	Function	DNA ligase activity	IMP	15871698
GO:0003909	Function	DNA ligase activity	TAS
GO:0003910	Function	DNA ligase (ATP) activity	IBA	21873635
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005739	Component	Mitochondrion	IBA	21873635
GO:0006266	Process	DNA ligation	IBA	21873635
GO:0006266	Process	DNA ligation	TAS
GO:0006273	Process	Lagging strand elongation	IBA	21873635
GO:0006281	Process	DNA repair	TAS	8696349
GO:0006283	Process	Transcription-coupled nucleotide-excision repair	TAS
GO:0006284	Process	Base-excision repair	IDA	19589734
GO:0006297	Process	Nucleotide-excision repair, DNA gap filling	TAS
GO:0006298	Process	Mismatch repair	TAS
GO:0009653	Process	Anatomical structure morphogenesis	TAS	8696349
GO:0033151	Process	V(D)J recombination	IDA	9809069
GO:0043231	Component	Intracellular membrane-bounded organelle	IDA
GO:0046872	Function	Metal ion binding	IEA
GO:0051301	Process	Cell division	IEA
GO:0071897	Process	DNA biosynthetic process	IEA
GO:1903461	Process	Okazaki fragment processing involved in mitotic DNA replication	IBA	21873635

Other IDs

• MIM: 126391
• HGNC: 6598
• e!Ensembl: ENSG00000105486

Protein

• UniProt ID: P18858
• Protein name: DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)
• Protein function: DNA ligase that seals nicks in double-stranded during DNA repair (PubMed:30395541). Also involved in DNA replication and DNA recombination.
• PDB: 1X9N, 5YY9, 6P09, 6P0A, 6P0B, 6P0C, 6P0D, 6P0E, 6Q1V, 7KR3, 7KR4, 7L34, 7L35, 7QNZ, 7QO1, 7SUM, 7SX5, 7SXE, 8B8T, 8VDN, 8VDS, 8VDT, 8VZL, 8VZM, 9BS3, 9BS4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04675	DNA_ligase_A_N	288 → 464	DNA ligase N terminus	Family
  PF01068	DNA_ligase_A_M	542 → 746	ATP dependent DNA ligase domain	Domain
  PF04679	DNA_ligase_A_C	771 → 882		Family

• Sequence:

  MQRSIMSFFHPKKEGKAKKPEKEASNSSRETEPPPKAALKEWNGVVSESDSPVKRPGRKA
  ARVLGSEGEEEDEALSPAKGQKPALDCSQVSPPRPATSPENNASLSDTSPMDSSPSGIPK
  RRTARKQLPKRTIQEVLEEQSEDEDREAKRKKEEEEEETPKESLTEAEVATEKEGEDGDQ
  PTTPPKPLKTSKAETPTESVSEPEVATKQELQEEEEQTKPPRRAPKTLSSFFTPRKPAVK
  KEVKEEEPGAPGKEGAAEGPLDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIE
  EVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQ
  ATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSAST
  AKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAM
  VDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPL
  KPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPD
  IISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAF
  DLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCE
  GLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLL
  ASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSA
  VWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQ
  SQIQNQQGEDSGSDPEDTY

• Sequence length: 919

Pathways

KEGG:

DNA replication
Base excision repair
Nucleotide excision repair
Mismatch repair

Reactome:

POLB-Dependent Long Patch Base Excision Repair
Early Phase of HIV Life Cycle
Processive synthesis on the C-strand of the telomere
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
PCNA-Dependent Long Patch Base Excision Repair
Gap-filling DNA repair synthesis and ligation in GG-NER
Gap-filling DNA repair synthesis and ligation in TC-NER
Processive synthesis on the lagging strand

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Colorectal cancer	Colorectal Carcinoma	rs137854568, rs137854573, rs137854575, rs387906234, rs121908380, rs121908702, rs267606674, rs794729661, rs121909055, rs281865417, rs267606884, rs28934575, rs587776769, rs104893815, rs587776800, rs63750198, rs63751109, rs863223312, rs63750710, rs63751615, rs63750206, rs63750781, rs63750899, rs63750691, rs63750217, rs121912965, rs63749939, rs63751194, rs63750693, rs63750540, rs63751221, rs193922370, rs80359596, rs397514632, rs483352909, rs200495564, rs397514684, rs397516436, rs398122386, rs79512956, rs74953290, rs587779001, rs63750677, rs63749837, rs267607816, rs63751715, rs267607819, rs267607815, rs267607822, rs63749906, rs587778883, rs63750472, rs63751012, rs63750715, rs63750580, rs267607706, rs267607709, rs267607710, rs587778894, rs63750749, rs63750483, rs63751015, rs63751153, rs63751094, rs63751118, rs63750316, rs63749981, rs587778906, rs267607821, rs587778908, rs63750020, rs587778909, rs63750713, rs267607825, rs63751592, rs281864936, rs587778913, rs587778914, rs63749795, rs63750855, rs63749916, rs63749923, rs63751472, rs63751689, rs267607832, rs267607837, rs267607836, rs587778923, rs63750028, rs587778928, rs587778929, rs587778930, rs63751277, rs587778933, rs267607842, rs267607843, rs63750192, rs587778934, rs63750193, rs587778937, rs587778938, rs267607845, rs63751244, rs63751393, rs63751460, rs267607849, rs267607853, rs267607856, rs267607850, rs63751657, rs267607854, rs267607852, rs587778942, rs63750309, rs63750587, rs63749863, rs63751486, rs63750016, rs63749868, rs63750375, rs63750035, rs63750604, rs63750386, rs63750150, rs63750486, rs63751428, rs267607866, rs63749986, rs63751594, rs63750152, rs63750850, rs267607867, rs267607868, rs63751632, rs267607871, rs63751892, rs587778956, rs63750469, rs587778958, rs63749792, rs267607875, rs63751255, rs281864938, rs63751202, rs63750726, rs63751310, rs63749900, rs587778964, rs267607879, rs267607878, rs587778966, rs267607883, rs267607887, rs63750061, rs63750663, rs587778968, rs587778971, rs63750809, rs63749867, rs63750864, rs587778972, rs63751275, rs267607718, rs267607722, rs63750769, rs267607717, rs587778973, rs267607716, rs267607720, rs63749995, rs63750859, rs587778975, rs63750114, rs587778976, rs63750603, rs267607889, rs267607723, rs63750561, rs63750499, rs63751642, rs63751022, rs587778981, rs63750971, rs267607898, rs267607906, rs267607903, rs587778989, rs587778992, rs267607894, rs267607901, rs267607892, rs63750437, rs587778997, rs587778998, rs63750005, rs63750641, rs63751421, rs11541859, rs63750266, rs111052004, rs267607726, rs267607727, rs63750453, rs267607734, rs267607735, rs63751665, rs267607736, rs267607732, rs63749816, rs63750539, rs267607739, rs587779006, rs587779008, rs267607745, rs267607742, rs63751595, rs267607743, rs587779010, rs587779012, rs63750057, rs63749818, rs63751124, rs587779014, rs587779015, rs63749820, rs63751302, rs267607750, rs267607751, rs267607749, rs63750891, rs63749959, rs63749804, rs267607765, rs267607760, rs587779021, rs267607759, rs63750515, rs587779023, rs63751021, rs63751480, rs267607772, rs267607773, rs587779024, rs63751653, rs587779027, rs267607767, rs587779029, rs63750706, rs63750385, rs267607774, rs267607778, rs267607780, rs587779034, rs63751711, rs267607784, rs587779035, rs63750823, rs63750822, rs267607787, rs63750303, rs63749839, rs63749827, rs267607789, rs267607790, rs267607791, rs267607786, rs267607771, rs267607795, rs267607794, rs267607788, rs267607799, rs267607801, rs587779045, rs63750034, rs587779047, rs63750216, rs63751707, rs63751598, rs267607803, rs267607777, rs63750144, rs267607805, rs63750547, rs63750489, rs63750993, rs587779054, rs63751259, rs63749926, rs63750796, rs587779058, rs63750745, rs63750582, rs180177084, rs587779866, rs200389141, rs587779950, rs587780104, rs587780183, rs587778536, rs587780683, rs587781554, rs267607712, rs587777627, rs587783057, rs730881734, rs41542214, rs730881273, rs786203456, rs786201990, rs786202767, rs748005072, rs786204317, rs786204318, rs797045117, rs63750549, rs863225383, rs863225384, rs863225373, rs863225376, rs863225377, rs863225378, rs863225379, rs863225380, rs863225381, rs63750059, rs267607823, rs864622457, rs869312767, rs869312753, rs876661059, rs876658915, rs876658923, rs876660860, rs876660822, rs876660458, rs876660214, rs876658657, rs876658247, rs876659226, rs876658821, rs876660589, rs876659068, rs876659681, rs876659608, rs878853794, rs878853778, rs878853780, rs878853785, rs886039423, rs886039424, rs1057517543, rs1057517541, rs756843954, rs1057517617, rs1057517558, rs1057519256, rs1060500689, rs764085979, rs1060500707, rs1060500699, rs1060500706, rs1060500703, rs1064795341, rs1064793607, rs1064794348, rs1064795441, rs1064794373, rs1064793172, rs1064794122, rs1064795515, rs1064794331, rs63750978, rs1114167435, rs1553641362, rs63751448, rs1553648029, rs1553648058, rs587778903, rs1553653237, rs1553664353, rs267607744, rs1553647995, rs1553648047, rs1553653084, rs1553663750, rs1553664436, rs1553488015, rs1553637293, rs63750310, rs63750443, rs63751596, rs1553646681, rs550890395, rs1064796057, rs1553642079, rs1553648023, rs587782087, rs746536721, rs1553653037, rs1248251121, rs1553646602, rs1434898623, rs1553665683, rs1553648068, rs1553645331, rs1553644123, rs1553658246, rs1553651299, rs1553648149, rs1553663159, rs1302248679, rs1553664119, rs1553658009, rs1553665977, rs1416171624, rs1553663834, rs1553664617, rs1553664702, rs1553647969, rs1553648040, rs1437454428, rs1553641273, rs63751101, rs1553646764, rs1553648225, rs1554082118, rs1553648201, rs1553638868, rs1553665866, rs376736188, rs1553642707, rs1553645226, rs1553652883, rs63751435, rs1553653115, rs1553653195, rs63750300, rs1553662622, rs1553658104, rs1553648220, rs1559544064, rs63750584, rs267608083, rs1559551570, rs1559575107, rs1559553501, rs1565986506, rs1559524405, rs1559553492, rs1559554339, rs1559588540, rs1559558071, rs761329565, rs1559521039, rs1559574795, rs1567221417, rs1559578422, rs1481129490, rs1570714352, rs779783209, rs1575376830, rs1575469070, rs1575537843, rs1575620443, rs1575621506, rs587779022, rs1575414904, rs1575449093, rs1575469505, rs1575536254, rs1575537933, rs1575632112, rs1575639851, rs1575441094, rs1575449402, rs267607831, rs2081922847, rs2083403132, rs2085415927, rs2085469647, rs2043913790, rs147542208

Unknown
Disease term	Disease name	Evidence	References	Source
Immunodeficiency	immunodeficiency 96			GenCC

Associations from Text Mining
Disease Name	Relationship Type	References
Agammaglobulinemia	Associate	30395541
Carcinoma Non Small Cell Lung	Associate	26125914, 30181552, 39231317
Carcinoma Squamous Cell	Associate	24929328
Colorectal Neoplasms Hereditary Nonpolyposis	Associate	31297992
DNA Virus Infections	Associate	24911150
Drug Related Side Effects and Adverse Reactions	Associate	34373746
Endometrial Neoplasms	Associate	21750170
Glioma	Associate	19124499
Hand Foot and Mouth Disease	Associate	33574876
Immune System Diseases	Associate	30395541, 39510190
Immunologic Deficiency Syndromes	Associate	30395541, 32914844
Lung Neoplasms	Associate	18059021, 18709642, 21976407, 22139380, 24929328, 30181552, 37369482
Lung Neoplasms	Stimulate	21976407
Lymphopenia	Associate	30395541
Macrocytosis Familial	Associate	30395541
Myelodysplastic Syndromes	Associate	23339595
Neoplasms	Inhibit	14520461
Neoplasms	Associate	39231317, 39234248
Neuroblastoma	Associate	25563294
Ovarian Neoplasms	Associate	34373746
Prostatic Neoplasms	Associate	37950047
Prostatic Neoplasms Castration Resistant	Stimulate	37950047
Severe Combined Immunodeficiency	Associate	36341401
Succinate Coa Ligase Deficiency	Inhibit	30395541
Succinate Coa Ligase Deficiency	Associate	36341401, 39510190
Syndrome	Associate	33444456
Triple Negative Breast Neoplasms	Associate	36001024
Urinary Bladder Neoplasms	Associate	32579540, 39234248
Uveal melanoma	Associate	30107825