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["Supplementary Table 4. CNVs Involving Exon 1"]
["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","H3K27Acf","TFM totalf","chromHMMg Ovary","Molecular Functionh","Biological Process (Urogenital, Reproductive)h","Full Location"]
["BBS9","Gain",3,30,12,"D21","exon 1 (RP9)","none (PIM1-binding)","1 (5')",2,1,"similar ","similar ","yes (2; 5' both genes)",8,"weak","BBSome assembly","ND","chr7:33148443-33178633"]
["CNTNAP3","Gain",3,95.708,17,"D15","exons 1-2","CNTNAP3, extracellular, F5/8 type C, signal peptide",1,"none ","none","mC+ ov","none (both)","yes (tall peaks on 5')","none ","none ","ND","ND","chr9:39247105-39342813"]
["NOTCH3","Gain",4,2.495,6,"D19","exon 1"," neurogenic locus notch3, extracellular, EGF-like, signal peptide","1 (5')","none ",1,"mC++ ov","RS++ adult","yes ",1,"none","calcium ion binding","glomerular capillary formation","chr19:15310066-15312561"]
["NOTCH3","Gain",4,2.786,9,"D16, D17, D18","exon 1"," neurogenic locus notch3, extracellular, EGF-like, signal peptide",1,"none ","1 (CGI 5' end)","none @ aTSS in both","different in 5', RS+ @3' in adult","yes ",1,"none","calcium ion binding","glomerular capillary formation","chr19:15309775-15312561"]
["NOTCH3","Gain",3,22.15,47,"D21","exons 1-20"," neurogenic locus notch3, extracellular, EGF-like, signal peptide",4,1,"2 (5', orphan)","different mC++","similar ","yes ","multiple","weak","calcium ion binding","glomerular capillary formation","chr19:15290411-15312561"]
["NR0B1","Gain",2,4.932,32,"D30","disrupted exon 1 ; exons 1-2","ligand binding, AF-2 motif, repeat, AA tandem repeats, LXXLL motif repeats",1,1,3,"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 and Sertoli cell differentiation, male sex determination, spermatogenesis, steroid metabolism","chrX:30322476-30327408"]
["NR5A1","Loss",1,18,5,"D9","exons 1-4 (NR6A1)","dimerization, ligand binding, phosphoserine, crosslinking, DNA binding, Zn finger, acetyllysine","1 (orphan intron 1-exons 2-3)","4 (intra, upstream of 5')",7,"mC+ ovary (CGI)","RS++ adult","yes (2)","multiple ","strong, weak","binding of chromatin, DNA, enzyme, phospholipid, Zn ion, transcription regulation, steroid hormone activity","development of adrenal gland and gonad, primary sex determination","chr9:127,261,935-127,279,829"]
["PCSK1","Loss",1,24.849,18,"D10","exons 1-3","neuroendocrine convertase 1, propep signal peptide","1 (5')",5,2,"similar (mC- ov tes)","different ","yes ",6,"RP, WRP","serine-type endopeptidase activity","cell-cell signaling, peptide hormone processing and synthesis, regulation of insulin secretion","chr5:95759422-95784271"]
["POR","Loss",1,15,9,"D23","exon 1","none ","1 (5', MIR4651)","2 (5', distal 5'; MIR4651)","1 (5')","different (5', distal enh)","different","yes (5)",6,"none","reductase activity, binding of iron, NADP","responsed to FSH, steroid synthesis","chr7:75532526-75547890"]
["PTCH1","Gain",4,4.356,20,"D42","exons 1-2","extracellular, transmembrane helical, cytoplasmic, gly-rich",1,"none",1,"none @ aTSS in both","similar ","yes ","multiple ","none","cholesterol, cyclin, hedgehog protein, heparin binding \n","development of the ureteric bud, kidney; cholesterol metabolism, mammary gland differentiation","chr9:98267551-98271907"]
["PTPN11","Loss",1,16.373,8,"D24","exon 1 (RPL6)","none ","1 (1)","none (1 genic)","yes (yes)","none @ aTSS in both (none @ aTSS)","different ","yes","1 (3) several upstream","none (strong, weak)","insulin receptor binding, phosphoprotein phosphatase activity \n","genitalia development, negative regulation of cortisol and growth hormone secretion ","chr12:112841387-112857760"]
["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)"]
["hND - no data in UniProt database for development of reproductive and urogenital structures"]