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Table 3 Summary of information collected and analyzed from different sources regarding HPin7 and HPin8 of DLG2

From: Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

  HPin7 HPin8 Reference Row
Human (hg19, DLG2)
 Location (UCSC) Intron 7 Intron 8 Fig. 1 1
 Number of del (DLG2 cohorta) 15 (29)b 16 (29)b Fig. 1 2
 Number of del GDD/ID cases 7 (14) 4 (14) Methods 3
 Number of del GDD/ID control 4 (19) 1 (19) Methods 4
 Number of del DGV 0 (24) 0 (24) Fig. S10c 5
 Number of del called from 1KG 0 (15) 2 (15) Fig. S11c 6
 Roadmap Epigenomics prediction Active promoter Active promoter Fig. S16, S17c 7
 Roadmap Epigenomics highest peak H3K4me3 in brain tissues H3K4me3 in brain tissues Fig. 2 8
 ncRNA lnc-TMEM126B-2:1 No Results 9
 FANTOM5 CAGE reads Yes Yes Fig. S30, S31c 10
 FANTOM5 CAGE expression Brain Brain Fig. S32c 11
 Number of human ESTs 2 2 Fig. S30, S31c 12
 Ensembl predicted DLG2 exon No Yes Table S2c 13
 ENCODE fetal brain RNA-Seq peaks Yes Yes Fig. S39, S40c 14
 JunctionSeq promoter and first exon de novo prediction Yes Yes Fig. S54c 15
 5′ splice site AG.GT AG.GT Fig. S43, S44c 16
 Coding exon Yes Yes Results 17
 Splicing into Exon 8 Exon 11 Results 18
 Recursive exon motif No No Results 19
Mouse (mm9, Dlg2)
 Location Intron 1 Intron 2 Fig S12, S13c 20
 Epigenomics (from ENCODE) H3K4me3 in cerebellum H3K4me3 in cerebellum Fig S12, S13c 21
 Ensembl exon prediction Yes Yes Fig S12, S13c 22
 Coding exon Yes Yes Results 23
 Splicing into Exon 2 Exon 4 Results 24
  1. For each source, a reference is reported. For rows 2–6, values in parentheses stand for the number of deletions overlapping the DLG2 7-9 region. Row 3: the number of total GDD/ID cases corresponds to the number of intragenic deletions, i.e., those that are not affecting other genes; hence, nssv_3460188 and nssv_3461505 are not considered (Additional file 1: Figure S6). The “5′ splice site” entry reports the two nucleotides before and after the exon–intron border (marked with the dot character)
  2. aThe DLG2 cohort is a collection of deletions from DECIPHER, ULB, and the literature overlapping the DLG2 7-9 region
  3. bFive deletions overlap both HPin7 and HPin8
  4. cIn Additional file 1