Protein: DNLI3
DNA ligase 3 (EC 6.5.1.1) (DNA ligase III) (Polydeoxyribonucleotide synthase [ATP] 3)

Gene: DNLI3, LIG3
Organism: Homo sapiens
Interactions: 214
UniProt ID: P49916

Gene Ontology (top 5):
GO:0000724 - double-strand break repair via homologous recombination
GO:0003677 - DNA binding
GO:0003909 - DNA ligase activity
GO:0003910 - DNA ligase (ATP) activity
GO:0005524 - ATP binding

Download interactions: TXT   MITAB-2.5

Interaction Interactor Experiments Homologs Category Interaction
Score
Confidence

557951

XRCC6
X-ray repair cross-complementing protein 6

5

6

Small-scale

0.932

High

617665

XRCC1
DNA repair protein XRCC1

14

0

Small-scale

0.930

High

487093

PARP1
Poly [ADP-ribose] polymerase 1

5

4

Small-scale

0.926

High

892641

PARP2
Poly [ADP-ribose] polymerase 2

2

2

High-throughput

0.776

High

559267

XRCC5
X-ray repair cross-complementing protein 5

1

6

Small-scale

0.724

High

892610

PNKP
Bifunctional polynucleotide phosphatase/kinase

5

3

Small-scale

0.718

High

588212

RFA2
Replication protein A 32 kDa subunit

5

1

High-throughput

0.714

High

892590

APLF
Aprataxin and PNK-like factor

5

1

Small-scale

0.709

High

892542

H31
Histone H3.1

5

2

High-throughput

0.702

High

446515

DPOLB
DNA polymerase beta

4

2

High-throughput

0.691

High

892633

RN146
E3 ubiquitin-protein ligase RNF146

5

0

Small-scale

0.679

High

892634

TYDP1
Tyrosyl-DNA phosphodiesterase 1

4

0

Small-scale

0.670

High

892601

H2B1A
Histone H2B type 1-A

3

4

High-throughput

0.667

High

892585

APTX
Aprataxin

3

3

Small-scale

0.650

High

259634

BRD4
Bromodomain-containing protein 4

3

3

High-throughput

0.640

High

892539

H2B1C
Histone H2B type 1-C/E/F/G/I

3

4

High-throughput

0.640

High

591537

H2AX
Histone H2AX

2

4

High-throughput

0.628

High

694936

RFA1
Replication protein A 70 kDa DNA-binding subunit

3

0

Small-scale

0.613

High

418887

H2A1B
Histone H2A type 1-B/E

2

4

High-throughput

0.611

High

892560

TOP3A
DNA topoisomerase 3-alpha

2

1

High-throughput

0.611

High

892623

WDR76
WD repeat-containing protein 76

2

1

High-throughput

0.611

High

892603

NEIL1
Endonuclease 8-like 1

2

0

Small-scale

0.606

High

501934

H2AZ
Histone H2A.Z

2

4

Small-scale

0.601

High

892564

MDC1
Mediator of DNA damage checkpoint protein 1

1

0

High-throughput

0.586

High

892635

TE2IP
Telomeric repeat-binding factor 2-interacting protein 1

1

0

High-throughput

0.586

High

278636

NDUS6
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

2

0

High-throughput

0.585

High

892579

PPCEL
Prolyl endopeptidase-like

2

0

High-throughput

0.585

High

892604

FMC1
Protein FMC1 homolog

2

0

High-throughput

0.585

High

892624

JMJD4
2-oxoglutarate and iron-dependent oxygenase JMJD4

2

0

High-throughput

0.585

High

892625

RSAD1
Radical S-adenosyl methionine domain-containing protein 1, mitochondrial

2

0

High-throughput

0.585

High

892647

NUDC
Nuclear migration protein nudC

2

1

High-throughput

0.584

High

767706

RFA3
Replication protein A 14 kDa subunit

2

0

High-throughput

0.559

High

892538

H4
Histone H4

2

0

High-throughput

0.559

High

429533

JUN
Transcription factor Jun

1

1

High-throughput

0.554

High

892535

MAX
Protein max

1

3

High-throughput

0.554

High

122991

KITM
Thymidine kinase 2, mitochondrial

1

1

High-throughput

0.536

High

133097

FOXE1
Forkhead box protein E1

1

5

High-throughput

0.536

High

166130

AIM2
Interferon-inducible protein AIM2

1

2

High-throughput

0.536

High

502272

H2A1
Histone H2A type 1

1

4

High-throughput

0.536

High

541892

TOP1
DNA topoisomerase 1

1

1

High-throughput

0.536

High

571574

IRF2
Interferon regulatory factor 2

1

1

High-throughput

0.536

High

892546

FOXK2
Forkhead box protein K2

1

5

High-throughput

0.536

High

892550

EMX2
Homeobox protein EMX2

1

1

High-throughput

0.536

High

892553

SSRP1
FACT complex subunit SSRP1

1

1

High-throughput

0.536

High

892557

RFA4
Replication protein A 30 kDa subunit

1

1

High-throughput

0.536

High

892562

DYR1A
Dual specificity tyrosine-phosphorylation-regulated kinase 1A

1

3

High-throughput

0.536

High

892567

NUMA1
Nuclear mitotic apparatus protein 1

1

1

High-throughput

0.536

High

892577

H2A2C
Histone H2A type 2-C

1

4

High-throughput

0.536

High

892578

H2B2E
Histone H2B type 2-E

1

4

High-throughput

0.536

High

892582

IFIX
Pyrin and HIN domain-containing protein 1

1

2

High-throughput

0.536

High

892593

H2B3B
Histone H2B type 3-B

1

4

High-throughput

0.536

High

892602

RN166
E3 ubiquitin-protein ligase RNF166

1

1

High-throughput

0.536

High

892611

FOXB1
Forkhead box protein B1

1

5

High-throughput

0.536

High

892621

FOXP1
Forkhead box protein P1

1

4

High-throughput

0.536

High

892627

CBX8
Chromobox protein homolog 8

1

5

High-throughput

0.536

High

892631

TF7L2
Transcription factor 7-like 2

1

3

High-throughput

0.536

High

892642

FOXD3
Forkhead box protein D3

1

5

High-throughput

0.536

High

892643

OGDHL
2-oxoglutarate dehydrogenase-like, mitochondrial

1

1

High-throughput

0.536

High

892651

SP16H
FACT complex subunit SPT16

1

1

High-throughput

0.536

High

573388

ENPL
Endoplasmin

1

2

High-throughput

0.515

High

892573

BRD3
Bromodomain-containing protein 3

1

2

High-throughput

0.515

High

74453

HNRC2
Heterogeneous nuclear ribonucleoprotein C-like 2

1

0

High-throughput

0.513

High

455728

H10
Histone H1.0

1

0

High-throughput

0.513

High

549299

SRF
Serum response factor

1

0

High-throughput

0.513

High

601598

HMGA1
High mobility group protein HMG-I/HMG-Y

1

0

High-throughput

0.513

High

837454

LAP2B
Lamina-associated polypeptide 2, isoforms beta/gamma

1

0

High-throughput

0.513

High

892531

HMGA2
High mobility group protein HMGI-C

1

0

High-throughput

0.513

High

892541

CSK2B
Casein kinase II subunit beta

1

0

High-throughput

0.513

High

892543

HMGN5
High mobility group nucleosome-binding domain-containing protein 5

1

0

High-throughput

0.513

High

892552

BAX
Apoptosis regulator BAX

1

0

High-throughput

0.513

High

892571

SYLM
Leucine--tRNA ligase, mitochondrial

1

0

High-throughput

0.513

High

892592

CMTR1
Cap-specific mRNA

1

0

High-throughput

0.513

High

892596

SPC24
Kinetochore protein Spc24

1

0

High-throughput

0.513

High

892608

TCPQM
T-complex protein 1 subunit theta-like 2

1

0

High-throughput

0.513

High

892613

MACD1
ADP-ribose glycohydrolase MACROD1

1

0

High-throughput

0.513

High

892619

NUCKS
Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1

1

0

High-throughput

0.513

High

892629

EXOS4
Exosome complex component RRP41

1

0

High-throughput

0.513

High

892646

ASC
Apoptosis-associated speck-like protein containing a CARD

1

0

Small-scale

0.513

High

725220

TLX1
T-cell leukemia homeobox protein 1

1

3

High-throughput

0.500

High

534795

BIP
Endoplasmic reticulum chaperone BiP

1

0

High-throughput

0.493

High

421733

A4
Amyloid-beta precursor protein

1

0

High-throughput

0.480

High

851463

GATA4
Transcription factor GATA-4

1

0

High-throughput

0.479

High

142895

NFIB
Nuclear factor 1 B-type

1

3

High-throughput

0.479

High

190852

RPA34
DNA-directed RNA polymerase I subunit RPA34

1

2

High-throughput

0.479

High

241099

PRKN
E3 ubiquitin-protein ligase parkin

1

3

High-throughput

0.479

High

285146

EED
Polycomb protein EED

1

3

High-throughput

0.479

High

340851

NFAC1
Nuclear factor of activated T-cells, cytoplasmic 1

1

1

High-throughput

0.479

High

352366

TOP3B
DNA topoisomerase 3-beta-1

1

1

High-throughput

0.479

High

362212

ABL1
Tyrosine-protein kinase ABL1

1

1

High-throughput

0.479

High

371484

MYC
Myc proto-oncogene protein

1

3

High-throughput

0.479

High

403914

GCR
Glucocorticoid receptor

1

5

High-throughput

0.479

High

405908

MYCN
N-myc proto-oncogene protein

1

3

High-throughput

0.479

High

411587

NTRK1
High affinity nerve growth factor receptor

1

1

High-throughput

0.479

High

473857

NFIC
Nuclear factor 1 C-type

1

4

High-throughput

0.479

High

504866

H2AB2
Histone H2A-Bbd type 2/3

1

4

High-throughput

0.479

High

519849

ANDR
Androgen receptor

1

4

High-throughput

0.479

High

533259

THA
Thyroid hormone receptor alpha

1

3

Small-scale

0.479

High

533329

THB
Thyroid hormone receptor beta

1

3

Small-scale

0.479

High

557178

SRC
Proto-oncogene tyrosine-protein kinase Src

1

1

High-throughput

0.479

High

567305

TCTP
Translationally-controlled tumor protein

1

1

High-throughput

0.479

High

606435

CEBPB
CCAAT/enhancer-binding protein beta

1

2

High-throughput

0.479

High

637003

VATB2
V-type proton ATPase subunit B, brain isoform

1

2

High-throughput

0.479

High

667213

RPB1
DNA-directed RNA polymerase II subunit RPB1

1

1

Small-scale

0.479

High

674110

BRD2
Bromodomain-containing protein 2

1

3

High-throughput

0.479

High

697041

APEX1
DNA repair nuclease/redox regulator APEX1

1

1

High-throughput

0.479

High

713955

PML
Protein PML

1

1

High-throughput

0.479

High

754765

H2B1B
Histone H2B type 1-B

1

4

High-throughput

0.479

High

789439

PPARG
Peroxisome proliferator-activated receptor gamma

1

4

Small-scale

0.479

High

851724

NKX21
Homeobox protein Nkx-2.1

1

3

High-throughput

0.479

High

855558

CRK
Adapter molecule crk

1

1

High-throughput

0.479

High

872078

SOX2
Transcription factor SOX-2

1

3

High-throughput

0.479

High

883484

CENPA
Histone H3-like centromeric protein A

1

2

High-throughput

0.479

High

892544

H33
Histone H3.3

1

2

High-throughput

0.479

High

892548

KIF23
Kinesin-like protein KIF23

1

1

High-throughput

0.479

High

892554

NFIA
Nuclear factor 1 A-type

1

3

High-throughput

0.479

High

892555

CHD3
Chromodomain-helicase-DNA-binding protein 3

1

1

High-throughput

0.479

High

892556

FOXC1
Forkhead box protein C1

1

5

High-throughput

0.479

High

892558

CBX3
Chromobox protein homolog 3

1

5

High-throughput

0.479

High

892559

NFAC2
Nuclear factor of activated T-cells, cytoplasmic 2

1

1

High-throughput

0.479

High

892565

CHD4
Chromodomain-helicase-DNA-binding protein 4

1

2

High-throughput

0.479

High

892566

NFIX
Nuclear factor 1 X-type

1

3

High-throughput

0.479

High

892570

TNIP1
TNFAIP3-interacting protein 1

1

1

High-throughput

0.479

High

892572

KIF14
Kinesin-like protein KIF14

1

1

High-throughput

0.479

High

892574

EEA1
Early endosome antigen 1

1

1

High-throughput

0.479

High

892575

EZH2
Histone-lysine N-methyltransferase EZH2

1

3

High-throughput

0.479

High

892576

IF16
Gamma-interferon-inducible protein 16

1

2

High-throughput

0.479

High

892584

TRI67
Tripartite motif-containing protein 67

1

2

High-throughput

0.479

High

892586

PARPT
Protein mono-ADP-ribosyltransferase TIPARP

1

1

High-throughput

0.479

High

892591

SMC5
Structural maintenance of chromosomes protein 5

1

1

High-throughput

0.479

High

892597

NUP43
Nucleoporin Nup43

1

1

High-throughput

0.479

High

892600

ESR2
Estrogen receptor beta

1

4

High-throughput

0.479

High

892605

UHRF2
E3 ubiquitin-protein ligase UHRF2

1

4

Small-scale

0.479

High

892607

CIC
Protein capicua homolog

1

3

High-throughput

0.479

High

892609

CRBN
Protein cereblon

1

1

Small-scale

0.479

High

892630

BRD7
Bromodomain-containing protein 7

1

2

High-throughput

0.479

High

892640

ZRAN1
Ubiquitin thioesterase ZRANB1

1

1

High-throughput

0.479

High

892650

TRRAP
Transformation/transcription domain-associated protein

1

3

High-throughput

0.479

High

128863

MEN1
Menin

1

0

High-throughput

0.458

High

157102

CTRO
Citron Rho-interacting kinase

1

0

High-throughput

0.458

High

222833

PRC1
Protein regulator of cytokinesis 1

1

0

High-throughput

0.458

High

247744

NUPR1
Nuclear protein 1

1

0

High-throughput

0.458

High

262040

NBN
Nibrin

1

0

Small-scale

0.458

High

298326

DNJC8
DnaJ homolog subfamily C member 8

1

0

High-throughput

0.458

High

301867

CLPX
ATP-dependent clpX-like chaperone, mitochondrial

1

0

High-throughput

0.458

High

385561

LMNA
Prelamin-A/C [Cleaved into: Lamin-A/C

1

0

High-throughput

0.458

High

413420

P53
Cellular tumor antigen p53

1

0

High-throughput

0.458

High

629664

BTF3
Transcription factor BTF3

1

0

High-throughput

0.458

High

699650

P85A
Phosphatidylinositol 3-kinase regulatory subunit alpha

1

0

High-throughput

0.458

High

731087

STIP1
Stress-induced-phosphoprotein 1

1

0

High-throughput

0.458

High

764551

CTNB1
Catenin beta-1

1

0

High-throughput

0.458

High

767135

MERL
Merlin

1

0

High-throughput

0.458

High

821263

TCPZ
T-complex protein 1 subunit zeta

1

0

High-throughput

0.458

High

843385

HD
Huntingtin

1

0

Small-scale

0.458

High

892530

MECP2
Methyl-CpG-binding protein 2

1

0

High-throughput

0.458

High

892532

ATX3
Ataxin-3

1

0

Small-scale

0.458

High

892533

EPHB4
Ephrin type-B receptor 4

1

0

High-throughput

0.458

High

892534

KLF3
Krueppel-like factor 3

1

0

High-throughput

0.458

High

892536

PSME3
Proteasome activator complex subunit 3

1

0

High-throughput

0.458

High

892537

RS6
Small ribosomal subunit protein eS6

1

0

High-throughput

0.458

High

892540

RL31
Large ribosomal subunit protein eL31

1

0

High-throughput

0.458

High

892545

HSF1
Heat shock factor protein 1

1

0

High-throughput

0.458

High

892549

NUCB1
Nucleobindin-1

1

0

High-throughput

0.458

High

892551

SUH
Recombining binding protein suppressor of hairless

1

0

High-throughput

0.458

High

892561

BIRC3
Baculoviral IAP repeat-containing protein 3

1

0

High-throughput

0.458

High

892569

SUZ12
Polycomb protein SUZ12

1

0

High-throughput

0.458

High

892581

RN123
E3 ubiquitin-protein ligase RNF123

1

0

High-throughput

0.458

High

892588

NAA40
N-alpha-acetyltransferase 40

1

0

High-throughput

0.458

High

892599

BAP1
Ubiquitin carboxyl-terminal hydrolase BAP1

1

0

High-throughput

0.458

High

892612

CND3
Condensin complex subunit 3

1

0

Small-scale

0.458

High

892614

DDX23
Probable ATP-dependent RNA helicase DDX23

1

0

High-throughput

0.458

High

892615

ACE2
Angiotensin-converting enzyme 2

1

0

High-throughput

0.458

High

892618

CCDC8
Coiled-coil domain-containing protein 8

1

0

High-throughput

0.458

High

892637

PD1L1
Programmed cell death 1 ligand 1

1

0

Small-scale

0.458

High

892638

HDAC6
Protein deacetylase HDAC6

1

0

High-throughput

0.458

High

892649

ZN330
Zinc finger protein 330

1

0

High-throughput

0.458

High

330080

VENTX
Homeobox protein VENTX

1

1

High-throughput

0.445

High

339956

RPA1
DNA-directed RNA polymerase I subunit RPA1

1

1

High-throughput

0.445

High

442898

PRGR
Progesterone receptor

1

5

Small-scale

0.445

High

765258

BMI1
Polycomb complex protein BMI-1

1

1

High-throughput

0.445

High

892589

CHD1L
Chromodomain-helicase-DNA-binding protein 1-like

1

2

High-throughput

0.445

High

892636

GRHL1
Grainyhead-like protein 1 homolog

1

2

High-throughput

0.445

High

560328

IFM1
Interferon-induced transmembrane protein 1

1

1

High-throughput

0.437

High

892547

IFM3
Interferon-induced transmembrane protein 3

1

1

High-throughput

0.437

High

892598

CLC4D
C-type lectin domain family 4 member D

1

2

High-throughput

0.437

High

892622

PKHA4
Pleckstrin homology domain-containing family A member 4

1

2

High-throughput

0.437

High

892645

CLC4E
C-type lectin domain family 4 member E

1

2

High-throughput

0.437

High

231551

PRKY
Putative serine/threonine-protein kinase PRKY

1

0

High-throughput

0.426

High

584076

FOSL2
Fos-related antigen 2

1

0

High-throughput

0.426

High

848763

MAGAA
Melanoma-associated antigen 10

1

0

High-throughput

0.426

High

892563

WRN
Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN

1

0

High-throughput

0.426

High

892580

LRRK2
Leucine-rich repeat serine/threonine-protein kinase 2

1

0

High-throughput

0.426

High

892587

HDGR2
Hepatoma-derived growth factor-related protein 2

1

0

High-throughput

0.426

High

892595

DTX3
Probable E3 ubiquitin-protein ligase DTX3

1

0

High-throughput

0.426

High

892616

REXO4
RNA exonuclease 4

1

0

High-throughput

0.426

High

892648

ITM2B
Integral membrane protein 2B

1

0

High-throughput

0.426

High

892583

CLC4G
C-type lectin domain family 4 member G

1

2

Small-scale

0.407

High

892606

SYGP1
Ras/Rap GTPase-activating protein SynGAP

2

0

High-throughput

0.313

High

391208

FRIL
Ferritin light chain

1

0

High-throughput

0.279

Low

630227

TNR1B
Tumor necrosis factor receptor superfamily member 1B

1

0

High-throughput

0.279

Low

692671

CALL3
Calmodulin-like protein 3

1

0

High-throughput

0.279

Low

892568

EMC2
ER membrane protein complex subunit 2

1

0

High-throughput

0.279

Low

892594

EMC5
ER membrane protein complex subunit 5

1

0

High-throughput

0.279

Low

892617

CF062
Uncharacterized protein C6orf62

1

0

High-throughput

0.279

Low

892632

ST7
Suppressor of tumorigenicity 7 protein

1

0

High-throughput

0.279

Low

892639

VPS29
Vacuolar protein sorting-associated protein 29

1

0

High-throughput

0.279

Low

67231

AN36A
Ankyrin repeat domain-containing protein 36A

1

0

High-throughput

0.249

Low

377462

INS
Insulin [Cleaved into: Insulin B chain; Insulin A chain]

1

0

High-throughput

0.249

Low

488746

FURIN
Furin

1

0

High-throughput

0.249

Low

619011

PLCG1
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1

1

0

High-throughput

0.249

Low

892626

RHOF
Rho-related GTP-binding protein RhoF

1

0

High-throughput

0.249

Low

892644

HECD1
E3 ubiquitin-protein ligase HECTD1

1

0

High-throughput

0.249

Low

58798

PIPSL
Putative PIP5K1A and PSMD4-like protein

1

0

High-throughput

0.232

Low

892620

CAD23
Cadherin-23

1

0

High-throughput

0.232

Low

892628

PTPRH
Receptor-type tyrosine-protein phosphatase H

1

0

High-throughput

0.232

Low


Service provided by Combinatics, Japan

Last updated: 11Aug2025