Table 1.
Chromosomal localization of HIV-derived vector integration sites with corresponding hit-RefSeq gene
| Integration | Frequencies* |
Gene name | Gene symbol | Gene ID | Distance to TSS, Kb | |||
|---|---|---|---|---|---|---|---|---|
| B1 | B2 | B4.1 | B4.2 | |||||
| b-01 | 15 (112) | 11 (60) | 2 (3) | 14 (15) | Similar to nsfl1 (p97) cofactor (p47) | LOC433885 | 433885 | −281 |
| b-02 | 6 (112) | - | - | - | Topoisomerase (dna) ii beta | Top2b | 21974 | 34 |
| b-03 | 3 (112) | - | - | - | Activated leukocyte cell adhesion molecule | Alcam (RIS) | 11658 | −493 |
| b-04 | 1 (112) | - | - | - | Similar to nsfl1 (p97) cofactor (p47) | LOC433885 | 433885 | −280 |
| b-05 | 4 (112) | - | - | - | Repeat seq.LINE | |||
| b-06 | 2 (112) | - | - | - | Similar to zinc finger, cchc domain containing 9 (predicted) | LOC383743 | 383743 | −144 |
| b-07 | 25 (112) | - | - | 1 (15) | Nudc domain containing 1 | Nudcd1 | 67429 | 6 |
| b-08 | 2 (112) | - | - | - | Similar to heterogeneous nuclear ribonucleoprotein c isoform b | LOC329893 | 329893 | −177 |
| b-09 | 5 (112) | - | - | - | Tbc1 domain family, member 15 | Tbc1d15 | 66687 | 20 |
| b-10 | 1 (112) | - | - | - | Septin 7 | Sept7 | 235072 | 49 |
| b-11 | 1 (112) | - | - | - | Repeat seq. SINE | |||
| b-12 | 1 (112) | - | - | - | Repeat seq. LTR | |||
| b-13 | 1 (112) | - | - | - | Repeat seq. LINE | |||
| b-14 | 1 (112) | - | - | - | Atpase, class vi, type 11b | Atp11b (RIS) | 76295 | 31 |
| b-15 | 2 (112) | - | - | - | Thymoma viral proto-oncogene 3 | Akt3 (RIS) | 23797 | 69 |
| b-16 | 4 (112) | - | - | - | Transient receptor potential cation channel, subfamily m, member 3 | Trpm3 | 226025 | 24 |
| b-17 | 2 (112) | - | - | - | Repeat seq. LINE | |||
| b-18 | 4 (112) | - | - | - | Ras association (RalGDS/AF-6) domain family (N-terminal) member 9 | RassF9 | 237504 | −235 |
| b-19 | 12 (112) | - | - | - | Transmembrane and tetratricopeptide repeat containing 3 | Tmtc3 | 237500 | 23 |
| b-20 | 5 (112) | 9 (60) | - | - | Zinc finger protein 804A | Zfp804a (RIS) | 241514 | −535 |
| b-21 | 8 (112) | 13 (60) | - | - | Repeat seq. LINE | |||
| b-22 | 5 (112) | 25 (60) | - | - | Cell adhesion molecule with homology to L1CAM | Chl1 | 12661 | −348 |
| b-23 | 1 (112) | - | - | - | Protection of telomeres 1A | Pot1a | 101185 | −1110 |
| b-24 | 1 (112) | 2 (60) | - | - | Zinc finger protein 804A | Zfp804a (RIS) | 241514 | −319 |
| b-25 | - | - | 1 (3) | - | Similar to svh protein | LOC382626 (RIS) | 382626 | −193 |
| F1 |
F2 |
F4.1 |
F4.2 |
|||||
|---|---|---|---|---|---|---|---|---|
| f-01 | 6 (59) | - | - | - | Riken cdna c730024g19 gene | C730024G19Rik | 232566 | −98 |
| f-02 | 1 (59) | - | 5 (16) | 3 (13) | Cerebellum postnatal development associated protein 2 | Cadps2 | 320405 | 488 |
| f-03 | 1 (59) | 39 (49) | 6 (16) | 9 (13) | Repeat seq. LINE | |||
| f-04 | 1 (59) | - | - | - | Repeat seq. SINE | |||
| f-05 | 1 (59) | - | - | - | Repeat seq. RNA | |||
| f-06 | 1 (59) | - | - | - | Yth domain family 3 | Ythdf3 | 229096 | 12 |
| f-07 | 1 (59) | - | - | - | Riken cdna 3830405g04 gene | 3830405G04Rik | 70681 | 2 |
| f-08 | 18 (59) | - | - | - | Riken cdna 1300010f03 gene | 1300010F03Rik | 219189 | 178 |
| f-09 | 1 (59) | - | - | - | Solute carrier family 4, sodium bicarbonate cotransporter, member 7 | Slc4a7 (RIS) | 218756 | 79 |
| f-10 | 3 (59) | - | - | - | Riken cdna 2610316d01 gene | 2610316D01Rik | 72511 | 14 |
| f-11 | 1 (59) | - | - | - | N-deacetylase/n-sulfotransferase 4-like | LOC545976 | 545976 | 37 |
| f-12 | 10 (59) | - | - | - | Myo3a myosin IIIA | Myo3a (RIS) | 667663 | −285 |
| f-13 | 13 (59) | - | - | - | Sorting nexin 13 | Snx13 | 217463 | 90 |
| f-14 | 1 (59) | - | - | - | Nuclear receptor coactivator 3 | Ncoa3 (RIS) | 17979 | 17 |
| f-15 | - | 2 (49) | - | - | Unknown region | |||
| f-16 | - | 8 (49) | - | - | Dynein cytoplasmic 1 intermediate chain 1 | Dync1i1 | 13426 | 193 |
| f-17 | - | - | 1 (16) | - | Zinc finger, a20 domain containing 3 | Za20d3 | 65098 | −5 |
| f-18 | - | - | 2 (16) | 1 (13) | Carbonic anhydrase 2 | Car2 | 12349 | 4 |
| f-19 | - | - | 2 (16) | - | Eukaryotic translation initiation factor 4e member 3 | Eif4e3 (RIS) | 66892 | −237 |
Distance to TSS indicates distance to transcription start site.
*
Numbers in this column indicate the number that each integration appears in the TopoTA analysis and numbers in parentheses correspond to all valid sequences in each analysis. One P96 multiwell was analyzed in all cases, except for primary recipients, in which 2 P96 were analyzed.