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Table 1 shRNA sense-stem/target sequences

From: The effects of stem length and core placement on shRNA activity

cnt

Hairpin

Target sequence covered (sense) a, b, c

16

Tat56 (15 - 41) d

A AACUGCUUGUACC A15AU U18G19C20U21A22U23U24G25U26A27A28A29gAG U33GUUG37CUUU41

6

Vpu10 (19 - 29)

A UAAUAGUAGCAAUAGUAG19CA21UU23AG25UA27GU29

6

Vpu51 (19 - 29)

A GCAAUAGUUGUGUGGUCC19AU21AG23UA25AU27CA29

6

Vpu127 (19 - 29)

G AUAGACUAAUAGAAAGAG19CA21GA23AG25AC27AG29

8

Vpu158 (17 - 29)

G CAAUGAGAGUGAAGGA17G18A19AG21UA23UC25AG27CA29

2

Tat3 (21, 29)

G GAGCCAGUAGAUCCUAGACU21AGAGCCCU29

4

Tat22/24 (21. 29)

C UA GAGCCCUGGAAGCAUCCU21GG21AAGUCA29GC29

2

Tat94 (21, 29)

U UUCAUUGCCAAGUUUGUUUC21AUAACAAA29

2

Tat144 (21, 29)

G CAGGAAGAAGCGGAGACAGC21GACGAAGA29

2

Tat165 (21, 29)

G ACGAAGAGCUCAUCAGAACA21GUCAGACU29

4

Tat181/187 (21, 29)

A ACAGUC AGACUCAUCAAGCU21UCUCUA21UCA29AAGCA29

5

(Tat56) 19+10 to 27+2

AAACUGCUUGUACCAAUUG19- {gauaacauuu+10 | CU21uaacauuu+8 | CUAU23acauuu+6 | CUAUUG25auuu+4 | CUAUUGUA27uu+2}

5

(Tat56) 10+19 to 2+27

{uuugacgaac10+ | uuugacga8+UG | uuugac6+CUUG | uuug4+UGCUUG | uu2+ACUGCUUG} -U11ACCAAUUGCUA UUGUAAA29

1

Tat59 21

C UGCUUGUACCAAUUGCUA UU21

9

(Tat59) 0-21-8 to 8-21-0

{_0 | u1 | uu2 | uuu3 | guuu4 | aguuu5 | gaguuu6 | ggaguuu7 | cggaguuu8} -CUGCUUGUACCAAUUGCUA UU(Tat59-21)- {cauuuggc8 | cauuugg7 | cauuug6 | cauuu5 | cauu4 | cau3 | ca2 | c1 | _0}

6

(Tat56) 23+6 {v2 - v7}

A AACUGCUUGUACCAAUUGCUA U23- { ggggggv2 | ccccccv3 | auauauv4 | gcgcgcv5 | gacuguv6 | acagucv7 }

8

(Tat56) 23+1 to 23+18 e

A AACUGCUUGUACCAAUUGCUA U23- {a24c25a26t27t28tgtca33aacg37aaag41}

92

  
  1. cnt : (count) the total number of new hairpins in each set (excluding hairpins already counted as a part of earlier sets).
  2. a : terminal nucleotides for each shRNA target/sense stem are indicated in bold, with the stem length indicated for each shRNA made.
  3. b : Sense stem sequence mismatched to the target is shown in lowercase. { a | b | c | etc. }: Continuing sequence where only one of the options was incorporated per shRNA.
  4. c : The binding region for the Tat56 19 nt. probe (for Northerns) is underlined.
  5. d : shRNA stem position 30 was changed in Tat56 33, 37 and 41 from 'A' to 'G' to prevent premature transcirptional termination from a run of 4 'T's.