IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell (0092-8674) 2012 imex curation Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., Singh H. Chromatin - Epigenetic interactions resulting in chromatin modulation ChIP data could not be captured as there are multiple Cyp3A and IgH genes. harindsi@gene.com Only protein-protein interactions in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa western blot western blot Immuno blot Immuno blot Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., Singh H. Chromatin - Epigenetic interactions resulting in chromatin modulation ChIP data could not be captured as there are multiple Cyp3A and IgH genes. GAGA motif-containing sequences were used as probes in an EMSA with nuclear extracts of NIH 3T3 transfected with a cKrox construct. Binding reactions containing NIH 3T3 nuclear extracts and the biotinylated probes were incubated with either streptavidin-coated or control agarose beads. The protein fractions bound to the beads were analyzed by western blot. harindsi@gene.com Accepted 2012-JUL-06 by JYOTI Cell (0092-8674) 2012 Only protein-protein interactions imex curation DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell (0092-8674) 2012 imex curation Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., Singh H. Chromatin - Epigenetic interactions resulting in chromatin modulation ChIP data could not be captured as there are multiple Cyp3A and IgH genes. harindsi@gene.com Only protein-protein interactions in vitro In vitro emsa supershift electrophoretic mobility supershift assay emsa supershift anti tag western anti tag western blot anti tag western Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., Singh H. Chromatin - Epigenetic interactions resulting in chromatin modulation ChIP data could not be captured as there are multiple Cyp3A and IgH genes. harindsi@gene.com Accepted 2012-JUL-06 by JYOTI Cell (0092-8674) 2012 Only protein-protein interactions imex curation DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell (0092-8674) 2012 imex curation Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., Singh H. Chromatin - Epigenetic interactions resulting in chromatin modulation ChIP data could not be captured as there are multiple Cyp3A and IgH genes. harindsi@gene.com Only protein-protein interactions mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., Singh H. Chromatin - Epigenetic interactions resulting in chromatin modulation ChIP data could not be captured as there are multiple Cyp3A and IgH genes. harindsi@gene.com Accepted 2012-JUL-06 by JYOTI Cell (0092-8674) 2012 Only protein-protein interactions imex curation igh_mouse_dna_1.1 Mouse IgH lamina-associating sequence ss dna single stranded deoxyribonucleic acid ss DNA ss dna mouse Mus musculus Mouse GAGGGAGAGAGAGGAAGACAGAGGAAGAGGAGGTGGAAG zbt7b_mouse Zinc finger and BTB domain-containing protein 7B Zinc finger protein 67 Zinc finger protein Th-POK T-helper-inducing POZ/Krueppel-like factor Krueppel-related zinc finger protein cKrox Zbtb7b Thpok Zfp67 protein protein mouse Mus musculus Mouse MGSPEDDLIGIPFPDHSSELLSCLNEQRQLGHLCDLTIRTQGLEYRTHRAVLAACSHYFKKLFTEGGGGTVMGTGGGGTASGGAGAGVCELDFVGPEALGALLEFAYTATLTTSSANMPAVLQAARLLEIPCVIAACMEILQGSGLEAPSPDEDDCERARQYLEAFATATTTASTSGMPNGEDSPPQVPLLPPPPPPPRPVARRSRKPRKAFLQTKGARANHLVPEAPTVLTHPLTYEEEEMVGRLGNSGGSGLGDSYSPPTGAASPAEGPLNYEVFEGEEEEEEMAYPPGYGLAQSNEPSLSPEELGSDEDPIDPDLMAYLSSLHQDALTPGLDGQDKLVRKRRSQMPQECPVCHKIIHGAGKLPRHMRTHTGEKPFACEVCGVRFTRNDKLKIHMRKHTGERPYSCPHCPARFLHSYDLKNHMHLHTGDRPYECHLCHKAFAKEDHLQRHLKGQNCLEVRTRRRRKDDVAAPHYPPPSTTTSSPAGLDLSNGHLDTFHLSLARFWEQSATTGPPVTTQGPPEEEEEEGTPTTPQAEGAMESS 5A43F10AE2970709 cyp3a_mouse_dna_5.1 Mouse Cyp3a lamina-associating sequence ss dna single stranded deoxyribonucleic acid ss DNA ss dna mouse Mus musculus Mouse ACATGTGGCCACAAATTGTTATCCGGTCACAATTGGACAT lap2b_mouse Lamina-associated polypeptide 2, isoforms beta/delta/epsilon/gamma Tmpo Lap2 Thymopoietin isoforms beta/delta/epsilon/gamma protein protein mouse Mus musculus Mouse MPEFLEDPSVLTKDKLKSELVANNVTLPAGEQRKDVYVQLYLQHLTARNRPPLAAGANSKGPPDFSSDEEREPTPVLGSGASVGRGRGAVGRKATKKTDKPRLEDKDDLDVTELSNEELLDQLVRYGVNPGPIVGTTRKLYEKKLLKLREQGTESRSSTPLPTVSSSAENTRQNGSNDSDRYSDNDEDSKIELKLEKREPLKGRAKTPVTLKQRRTEHNQSYSQAGVTETEWTSGSSTGGPLQALTRESTRGSRRTPRKRVETSQHFRIDGAVISESTPIAETIKASSNESLVANRLTGNFKHASSILPITEFSDITRRTPKKPLTRAEVGEKTEERRVDRDILKEMFPYEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYAPLADVKSEKTKKRRSVPMWIKMLLFALVAVFLFLVYQAMETNQGNPFTNFLQDTKISN 132AF11B458DCFBA hdac3_mouse Histone deacetylase 3 Hdac3 protein protein mouse Mus musculus Mouse MAKTVAYFYDPDVGNFHYGAGHPMKPHRLALTHSLVLHYGLYKKMIVFKPYQASQHDMCRFHSEDYIDFLQRVSPTNMQGFTKSLNAFNVGDDCPVFPGLFEFCSRYTGASLQGATQLNNKICDIAINWAGGLHHAKKFEASGFCYVNDIVIGILELLKYHPRVLYIDIDIHHGDGVQEAFYLTDRVMTVSFHKYGNYFFPGTGDMYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVISQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRGHGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTRIENQNSRQYLDQIRQTIFENLKMLNHAPSVQIHDVPADLLTYDRTDEADAEERGPEENYSRPEAPNEFYDGDHDNDKES DIP protein O88895 original sequence version: 74 DIP protein O88895 original sequence version: 89 DIP protein O88895 original sequence version: 92 DIP protein O88895 original sequence version: 104 DIP protein O88895 original sequence version: 138 DIP protein O88895 original sequence version: 135 DIP protein O88895 original sequence version: 105 DIP protein O88895 original sequence version: 111 B0C3BB2C5CD95E0E igh_mouse_dna_1.4 Mouse IgH lamina-associating sequence ss dna single stranded deoxyribonucleic acid ss DNA ss dna mouse Mus musculus Mouse ACAGGTGCAGAGGAAGATCTGGAGAGTGAGAGTGAGGCAG cyp3a_mouse_dna_5.6 Mouse Cyp3a lamina-associating sequence ss dna single stranded deoxyribonucleic acid ss DNA ss dna mouse Mus musculus Mouse CCTTCTCTTTATCATTCTCTCCCTCCTTCTTTCCCTCTCT zbtb7b-cyp3a 2 6 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells physical association physical association Fig. 5C The complexes were supershifted with an anti-Myc antibody and were not formed if the GAGA motif was mutated to CACA zbtb7b-igh 2 4 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells physical association physical association Fig. 5C The complexes were supershifted with an anti-Myc antibody and were not formed if the GAGA motif was mutated to CACA zbtb7b-cyp3a-2 1 5 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells 6 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 8 unspecified role unspecified role prey prey mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells association association Fig. 5D, 5E zbtb7b-hdac3 1 4 unspecified role unspecified role prey prey region biotin tag biotin tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells 8 unspecified role unspecified role prey prey mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells association association Fig. 5D, 5E The complexes were supershifted with an anti-Myc antibody and were not formed if the GAGA motif was mutated to CACA zbtb7b-cyp3a-3 1 10 unspecified role unspecified role prey prey chemical synthesis Chemical synthesis (Chemical synthesis) 5 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells 8 unspecified role unspecified role prey prey mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells association association Fig. 5D, 5E zbtb7b-hdac3-1 1 5 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells 8 unspecified role unspecified role prey prey mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells 9 unspecified role unspecified role prey prey chemical synthesis Chemical synthesis (Chemical synthesis) association association Fig. 5D, 5E The complexes were supershifted with an anti-Myc antibody and were not formed if the GAGA motif was mutated to CACA zbtb7b-hdac3-2 3 5 unspecified role unspecified role bait bait 8 unspecified role unspecified role prey prey 7 unspecified role unspecified role prey prey association association Fig. 6A lap2b-zbtb7b 3 5 unspecified role unspecified role prey prey 7 unspecified role unspecified role bait bait physical association physical association Fig. 6A lap2b-hdac3 3 8 unspecified role unspecified role prey prey 7 unspecified role unspecified role bait bait association association Fig. 6A