Fig 1.
The sequence of the Translocation Breakpoint Type A (TBTA) is from GenBank sequence ID:AB261997.1 [13].
The figure shows the HSATI, Alu, AT-rich regions and the PATRR. Positions 1–306 represent a direct repeat of 814–1119. Positions of Satellite/Alu/AT-rich regions in the translocation breakpoint type A sequence were determined by RepeatMasker analysis).
Table 1.
Satellite/Alu/AT-rich positions in TBTA.
Table 2.
Satellite/Alu/ Repeat in human satellite I.
Table 3.
Satellite/Alu/AT-rich regions of FAM230C, positions 17010–22032*.
Fig 2.
Alignment of the TBTA sequence with lincRNA gene FAM230C sequence, which encompasses repeat #3 in FAM230C (Table 3).
The nucleotide positions in both sequences are shown. The NCBI Align Two Sequences Nucleotide BLAST program was used.
Fig 3.
Diagrammatic representation of the 22q11.2 region showing positions of LCR22A-D and lincRNA genes #1–7 that carry the TBTA and are listed in Materials and Methods.
22q11.2 coordinates are from Guna et al [31] and LCR22A-D coordinates from Demaerel et al [32]. Line drawings that represent chromosomal distances, LCR22 positions and lincRNA gene positions are approximate.
Table 4.
Properties of lincRNA genes in chr22.
Fig 4.
Sequence alignment of LINC01660 (AC011718.2) lincRNA gene sequence with FAM230C and TBTA sequences.
sequences. The figure shows the similarity of the LINC01660 (AC011718.2) sequence with that of the TBTA and extends from approximately the middle of the PATRR (TBTA position 1686) to the 3’ end of the TBTA (position 2540). Excluding the AT-variable sequences and a PATRR sequence rearrangement, the entire TBTA sequence is found in LINC01660. Clustal Omega Multiple Sequence Alignment program (EMBL-EBI) was used for alignment.
Table 5.
Satellite/Alu/AT-rich regions of LINC01660 (AC011718.2)*.
Fig 5.
Sequences surrounding gene AC007731.1 on chr 22 Top: Alignment of FAM230C, AC007731.1 and chr 22 sequences.
The sequences in sections B. and C. (highlighted in yellow) are outside of but contiguous with the AC007731.1 gene. Bottom: schematic of regions A, B, and C (highlighted in yellow) that represent the close identity of FAM1230C sequences with those of chr22. The sequence in chr 22 that has a high identity with FAM230C and is contiguous with the 5' side of AC007731.1, region B. is ~389 bp long and the FAM230C sequence contiguous on the 3' side of AC007731.1, region C. is ~150 bp. The upstream region of AC007731.1 termed A., consists of 2711 bp segment of chr22 that has a high identity with 5’ half sequences of FAM230C.