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["Supplementary Table 3. CNVs with Breakpoints Disrupting Exons"]
["Gene","Type","CN State","CNV Size (Kb)","Marker Count","ID #a","Exonsb","Protein Annotation","CGIc","with enhancers","with active TSS","methylC-seqd ovary vs testis","RNA-Seqe fetal vs adult ovary","H3K27Ac peaks","TFM totalf","chromHMMg Ovary","Molecular Function","Biological Process (Urogenital, Reproductive)","Full Location"]
["CXCL12","Gain",4,6.895,10,"D17","exon 4 (3')","none ","none ","1  (distal 3')","none","mC+ testis (enhancer 5' distal)","similar ","yes ",1,"strong, weak ","chemokine activity and receptor binding ","germ cell development and migration, patterning of blood vessels","chr10:44861362-44868257"]
["ESR2","Gain",3,1.805,26,"D15, D16","exon 13 ","disrupted steroid-binding ","none",1,"none ","mC+ in testis (enhancer)","different ","yes ","1 (intron 12)","weak ","estrogen receptor activity, DNA binding","estrogen receptor signaling pathway","chr14:64701750-64703555"]
["FLNA","Gain",2,16.012,37,"D21","exon 22 (exons 22-48)","hinge 2, repeats, N6-acetyllysine, modification, phosphoprotein, hinge 1, Int: furin; disrupted FLNA, filamin 11 repeat","2 orphans","none ","none ","similar ","similar ","none ","multiple ","strong, weak","actin filament, glycoprotein  \npoly(A) RNA, GTPase, transcription factor binding;  homodimerization; signal transduction","cytoskeleton organization, mesenchymal transition","chrX:153572560-153588572"]
["FLNA","Gain",2,10.732,23,"D9","exon 48","N6-acetyllysine; disrupted hinge 2, FLNA, repeat","2 orphans (3' distal)","none ","none ","mC+ ov (distal CGI)","different ","yes ",2,"weak","actin filament, glycoprotein  \npoly(A) RNA, GTPase, transcription factor binding;  homodimerization; signal transduction","cytoskeleton organization, mesenchymal transition","chrX:153566595-153577327"]
["INSR","Loss",1,29.054,23,"D14","exon 22 (ZNF557)","none ","1 (distal 3' bw INSR ZNF557)",1,"none ","mC+ testis INSR, none in CGI (both) ","RS++ fetal","yes ",8,"weak (ZNF557 Zn genes repeats, heterochromatin)","nucleotide, insulin and receptor binding, protein tyrosine kinase activity \n","development of adrenal gland, and male and female gonads, male sex determination, insulin receptor signaling","chr19:7083628-7112682"]
["KRAS","Gain",3,4.197,20,"D2","exon 4","GTP-binding site; disrupted GTPase Kras N-terminally processed, GTPase KRAS, helix","none","none","none ","similar ","similar ","none ","none ","weak","guanoside and protein complex binding","insulin, endocrine and EGFR signaling, steroid metabolism","chr12:25374464-25378661"]
["KRAS","Gain",3,12.167,35,"D7","exon 4 (exons 4-5)","GTP-binding site, propep, lipidation, modification, hypervariable region; disrupted GTPase Kras N-terminally processed, GTPase KRAS, helix","none","none","none ","similar","none (both)","none ","none ","weak","guanoside and protein complex binding","insulin, endocrine and EGFR signaling, steroid metabolism","chr12:25366494-25378661"]
["KRAS","Gain",3,8.5,29,"D6, D19","exon 4","GTP-binding site; disrupted GTPase Kras N-terminally processed, GTPase KRAS, helix","none","none","none ","similar","none (both)","none ","none ","weak","guanoside and protein complex binding","insulin, endocrine and EGFR signaling, steroid metabolism","chr12:25370161-25378661"]
["NR0B1","Gain",2,4.932,32,"D30","exon 1 (exons 1-2)","ligand binding, AF-2 motif, repeat, LXXLL motif repeats; disrupted AA tandem and 1 repeats","1 (disrupted)",1,3,"mC+ ov (CGI)","similar","none ",2,"WRP","DNA, RNA, protein domain binding;  steroid hormone receptor binding and activity; transcription regulation","development of male gonad and adrenal gland, Leydig cell differentiation, male sex determination, Sertoli cell differentiation, spermatogenesis, steroid metabolism","chrX:30322476-30327408"]
["PDGFRA","Gain",3,2.859,22,"D6","exon 23 ","phosphoprotein, ser-rich; disrupted PDGFRA and cytoplasmic","none ","none ","none ","similar ","similar ","none ","none ","strong ","ATP binding, PDGFRA binding and activity, transmembrane kinase activity, VEGFRA binding and activity \n","estrogen metabolic process, Leydig cell differentiation, luteinization, development of adrenal gland and male genitalia, \nmetanephric glomerular capillary formation","chr4:55156537-55159396"]
["SRD5A2","Loss",1,6.909,8,"D30, D39","exon 6 (exons 4-6)","disrupted transmembrane","none ","none","none","similar","different ","none ","none ","none","steroid activity, amide binding \n","androgen and other steroid metabolism, development of gonad and genitalia, response to FSH and testosterone","chr2:31750615-31757524"]
["ahighlighted ID# recurrent CNVs in 2 patients "]
["bgene in a parenthesis - another gene included in the CNV"]
["cCGI - CpG island"]
["dmC - methyl-C profile for DNA (CGI methylation) - mC+ (present)"]
["eRNA-seq - RS++ (higher), RS+ (present), RS- (absent) predicted RNA expression "]
["fentry in parenthesis - number or location of peaks"]
["gChromHMM - ChIP Seq data for predicting chromatin states (strong or weak transcription; WRP/RP, weak/repressed polycomb)"]