Skip to main content
. 2019 Feb 7;145(2):401–414. doi: 10.1002/ijc.32114

Table 1.

Events detected by STAR in RAD51C with RNA‐seq compared to the reference sequence NM_058216

Genomic coordinates start and end1 Event description HGVS nomenclature Biotype Functional Annotation2 Read counts CE3 Davy et al.3 G/E4
Targeted‐LCLs5 LCLs breast fimbria
56,769,994 56,772,291 Δ1q156 r.‐11_145del donor shift Non‐coding 1,172 28 12 6 Y Y GE
56,769,994 56,770,711 Δ1q156+▾1A r.‐11_145del+r.145_146ins145+563_145+862 mixed PTC‐NMD 62 0 0 2 Y N G
56,770,047 56,772,291 Δ1q103 r.43_145del donor shift PTC‐NMD 3,777 80 82 26 Y Y GE
56,770,047 56,770,711 Δ1q103+▾1A r.43_145del+r.145_146ins145+563_145+862 mixed PTC‐NMD 125 4 1 0 Y Y G
56,770,047 56,772,294 Δ1q103_Δ2p3 r.43_148del mixed PTC‐NMD 31 2 1 0 Y Y
56,770,047 56,774,053 Δ1q103_Δ2 r.43_404del mixed PTC‐NMD 40 0 0 0 N N
56,770,321 56,772,291 ▾1q171 r.145_146ins145+1_145+171 donor shift PTC‐NMD 272 7 1 0 Y Y
56,770,480 56,772,291 ▾1q330 r.145_146ins145+1_145+330 donor shift PTC‐NMD 59 0 0 0 N N G
56,770,150 56,770,711 ▾1Aa300 r.145_146ins145+563_145+862 cassette PTC‐NMD 401/571 23/20 6/3 0 Y Y GE
56,771,173 56,772,291 ▾1Ab461 r.145_146ins145+563_145+1,023 cassette PTC‐NMD 401/723 23/21 6/10 0 Y Y GE
56,770,150 56,772,294 Δ2p3 r.146_148del acceptor shift No FS 187 1 0 0 Y Y
56,770,150 56,774,053 Δ2 r.146_404del cassette PTC‐NMD 788 0 2 0 Y Y GE
56,772,376 56,774,053 Δ2q175 r.230_404del donor shift PTC‐NMD 19 0 0 0 Y N
56,772,529 56,774,053 Δ2q22 r.383_404del donor shift PTC‐NMD 24 0 0 0 Y N
56,772,551 56,780,556 Δ3 r.405_571del cassette PTC‐NMD 372 63 2 0 Y Y GE
56,772,551 56,787,219 Δ3,4 r.405_705del multicassette PTC‐NMD 67 0 0 0 N N
56,772,578 56,774,053 ▾2q27 r.404_405ins404+1_404+27 donor shift PTC‐NMD 553 9 0 0 Y Y
56,774,221 56,776,553 ▾3A (alternative 3′ end) r.571_572ins571+2334_571+3,395+r.572_1131del Terminal modification intronic STOP+polyA 15/− 0/− 0/− 0/− ‐ N
56,774,221 56,777,235 ▾3B (alternative 3′ end) r.571_572ins571+3016_571+3,394+r.572_1131del Terminal modification intronic STOP+polyA 310/− 18/− 6/− 0/− ‐ Y GE
56,774,221 56,780,637 Δ4p81 r.572_652del acceptor shift No FS 178 5 1 0 Y Y
56,774,221 56,780,667 Δ4p111 r.572_682del acceptor shift No FS 32 1 0 0 N N
56,774,221 56,787,219 Δ4 r.572_705del cassette PTC‐NMD 444 10 0 0 Y Y
56,774,221 56,798,106 Δ4,5 r.572_837del multicassette PTC‐NMD 17 0 0 0 Y N
56,774,221 56,783,238 Δ4,▾4A145 r.572_705del+r.705_706ins705+2549_705+2,693 mixed PTC‐NMD 17 2 0 0 Y Y
56,780,691 56,783,238 ▾4A145 r.705_706ins705+2549_705+2,693 cassette PTC‐NMD 4144/4016 233/180 8/0 12/0 Y Y GE
56,780,691 56,783,849 ▾4B120 r.705_706ins705+3160_706–3,251 cassette PTC‐NMD 456/332 28/24 1/1 0/0 Y Y GE
56,780,691 56,785,151 ▾4C48 r.705_706ins706‐2068_706–2021 cassette No FS 25/34 1/1 0/0 0/0 Y N
56,780,691 56,798,106 Δ5 r.706_837del cassette No FS 38 0 0 0 Y Y
56,787,352 56,787,956 ▾5A57 r.837_838ins837+606_837+662 cassette PTC‐NMD 161/54 22/10 0/0 0/0 Y N
56,787,352 56,791,366 ▾5B75 r.837_838ins837+4,016_837+4,089 cassette No FS 36/4 0/0 0/0 0/0 Y N
56,787,352 56,797,876 ▾5C100 r.837_838ins838‐230_838–131 cassette PTC‐NMD 881/327 29/24 5/1 0/2 Y Y
56,787,352 56,797,928 ▾5D48 r.837_838ins838‐178_838–131 cassette PTC‐NMD 199/327 0/24 0/1 0/2 Y N
56,787,352 56,801,400 Δ6 r.838_904del cassette PTC‐NMD 200 6 0 0 Y Y GE
56,787,352 56,809,844 Δ6,7 r.838_965del multicassette PTC‐NMD 397 1 0 0 Y Y
56,787,352 56,809,841 Δ6,7+▾8p3 r.838_965del+r.965_966ins966‐3_966–1 mixed PTC‐NMD 153 0 2 0 Y Y
56,787,352 56,811,478 Δ6_8 r.838_1026del multicassette No FS 81 3 0 0 Y Y
56,798,174 56,801,378 ▾7p22 r.904_905ins905‐22_905–1 acceptor shift PTC‐NMD 39 0 0 0 Y N
56,798,174 56,809,844 Δ7 r.905_965del cassette PTC‐NMD 3,382 48 7 2 Y Y GE
56,798,174 56,809,841 Δ7+▾8p3 r.905_r.965del+r.965_966ins966‐3_966–1 mixed PTC‐NMD 227 1 0 0 Y Y G
56,798,174 56,811,478 Δ7,8 r.905_1026del multicassette PTC‐NMD 677 5 1 0 Y Y GE
56,801,462 56,803,052 ▾7A72 r.965_966ins965+1592_965+1,663 cassette PTC‐NMD 46/39 23/13 0/0 0/0 Y N
56,801,462 56,807,546 ▾7B122 r.965_966ins966‐2298_966–2,177 cassette PTC‐NMD 612/1091 18/23 3/2 2/0 Y Y G
56,807,669 56,809,841 ▾7B122+▾8p3 r.965_966ins966‐2298_966–2,177+r.965_966ins966‐3_966–1 mixed PTC‐NMD 48 0 0 2 Y Y
56,801,462 56,809,841 ▾8p3 r.965_966ins966‐3_966–1 acceptor shift No FS 3,381 84 14 10 Y Y GE
56,801,462 56,811,478 Δ8 r.966_1026 cassette PTC‐NMD 49 3 0 0 Y Y
56,809,906 56,811,484 Δ9p6 r.1027_1032del acceptor shift No FS 21 1 0 0 Y N

Combination of individual splicing events was inferred from CE‐data.

1

Genomic coordinates on chr 17, human genome built GRCh37.

2

PTC‐NMD, premature‐stop codon‐ nonsense mRNA‐mediated decay; FS, frameshift.

3

Y, event was found; N, event was not found. ‐: not tested.

4

Events described in Gencode or Ensemble are shown with a G or E, respectively. GE is used if an event is described in both databases.

5

Read counts are shown as the average or read counts in the 4 samples. 2 numbers are shown for inserted exons.