Annotated gene sequence

Experiment = in vivo icSHAPE / NAI-N3 RefSeq = hg38 Cell = HEK293T Original Data Reference = Cell. 2016;165(5):1267-1279.

stable secondary structure loop bulge/internal loop no SHAPE data coding sequence

CGGATTTTTATGAGATATAATTACATTGACATGACGCCTCATGATTTACCCATGACTCGGGGGGTTTCCAAACTCCAAACACCTCCAGACTGGAGCCCGT
CAATCAGCTTCCTCTTGCTTTTCGTGGACTCCCACTGTGGAAACCTGCTGGTGTTTTGCTGCGGTTTCATTTCCCTCTGCGGAGGAGCCAGGGCAACCTT
GGCCAGACAGGCACCTAGCTGTGCCCTTCTTTCCAGGGCCTCTTCTCCACTCAGCTGACTCCCCTGGCCTGCCTAACGCTCCTGACTGAGACGGTTTTCC
GGCTTCCTCTAACAGGTTGGCGGGAAGTTGATCTGCAAACGCGAGGCAAAGCAGGAGTGTCCTTATTCGGTAGGCCTCTGATGGGCCACCAGAGCCGTCC
GAAAGTCCTAGCGGAGTGATTGACAGTGGCCATTTCAAAGCCTGAGTTCACCTTCTTTGCAACCACAATCACGACCCAGAATAAACTGCTTCCTGGAAGC
CGGCTAGTTGCACCTGGCCTGAAGTCAGTCTCGGGACTGCCTCTCAGGACCCCAGACAGGGTTTCGGGTTCCCGCCTGGGTCACGTGTACGGAGGCTGCC
AGTGCGCACTCAGCCCGGCCCGCCGGTCGCCACAGCAACACCAATCCCGGGTTCAAGCCCGCCTAGGAAGTGCGGTCCCCGCCTGACCGCCCCGGGCTTA
AGGGAGCCTGGCTAGGCCGGCAGCCGGATGGTCCCGCAGCTCGGGGCCGGCCATGCTTCGCGGTCCGTGGCGCCAGCTTTGGCTCTTTTTCCTGCTGCTG
CTCCCGGGCGCGCCTGAGCCCCGCGGCGCCTCCAGGCCGTGGGAGGGAACCGACGAGCCGGGCTCGGCCTGGGCCTGGCCGGGCTTCCAGCGCCTGCAGG
AGCAGCTCAGGGCGGCGGGTGCCCTCTCCAAGCGGTACTGGACGCTCTTCAGCTGCCAGGTGTGGCCCGACGACTGTGACGAGGACGAGGAGGCAGCCAC
GGGGCCCCTGGGCTGGCGCCTTCCTCTGTTGGGCCAGCGGTACCTGGACCTCCTGACCACGTGGTACTGCAGCTTCAAAGACTGCTGCCCTAGAGGGGAT
TGCAGAATCTCCAACAACTTTACAGGCTTAGAGTGGGACCTGAATGTGCGGCTGCATGGCCAGCATTTGGTCCAGCAGCTGGTCCTAAGAACAGTGAGGG
GCTACTTAGAGACGCCCCAGCCAGAAAAGGCCCTTGCTCTGTCGTTCCACGGCTGGTCTGGCACAGGCAAGAACTTCGTGGCACGGATGCTGGTGGAGAA
CCTGTATCGGGACGGGCTGATGAGTGACTGTGTCAGGATGTTCATCGCCACGTTCCACTTTCCTCACCCCAAATATGTGGACCTGTACAAGGAGCAGCTG
ATGAGCCAGATCCGGGAGACGCAGCAGCTCTGCCACCAGACCCTGTTCATCTTCGATGAAGCGGAGAAGCTGCACCCAGGGCTGCTGGAGGTCCTTGGGC
CACACTTAGAACGCCGGGCCCCTGAGGGCCACAGGGCTGAGTCTCCATGGACTATCTTTCTGTTTCTCAGTAATCTCAGGGGCGATATAATCAATGAGGT
GGTCCTAAAGTTGCTCAAGGCTGGATGGTCCCGGGAAGAAATTACGATGGAACACCTGGAGCCCCACCTCCAGGCGGAGATTGTGGAGACCATAGACAAT
GGCTTTGGCCACAGCCGTCTTGTGAAGGAAAACCTGATTGACTACTTCATCCCCTTCCTGCCTTTGGAGTACCGTCACGTGAGGCTGTGTGCACGGGATG
CCTTCCTGAGCCAGGAGCTCCTGTATAAAGAAGAGACACTGGATGAAATAGCCCAGATGATGGTGTATGTCCCCAAGGAGGAACAACTCTTTTCTTCCCA
GGGCTGCAAGTCTATTTCCCAGAGGATTAACTACTTCCTGTCATGAAGGCTAGAGGAAGACTTCCTGGAACTGCCTTTCTTCCACTAACAGGACCCTGGG
ACCTGTAGGAGCACCCCGTTTGGGACTGTGAGGTGTTTGAGGGTGTGGACTGGCATCCAGCAGCCACTAACAAACACACAACTGGTGTGTAAAAGGCAGG
CCTTACATTAGAAGCCAAGCCAATCCTTTTTCTTTTTTTTGGAGGTCCCACCGAGATAGATAGGAACTTGGATTGCTGAATTCAAAAACAGAGCCCATTC
TTAAGATCACTTGGTGCCTTAAAGACACGCATTCCAAAGTGGAATGTGGTTGAAGAAAGTGGGCCAGGTGGTTGAAGAAAGCCATGTGGGAGCTCAGCAA
ATCCCAAGGGCTTATTATGACACTCCAGATGGTCTCCTTAGCATCTCAGCTCTTCTGCAAGGAAGAGCTTGGGTGTTAGGCCTCAGAGGCTGTAGGGTCC
TTGGGTTACAGAGCCGGGGAGAACGAAGTTCTGTGACCCAGGGGTGGAGAATACACTCTAGGTTTGCAGGCTGGTGGGCTTTCAAATTGGTACTTCCAGA
GGAAAGCCAAGCTGCTTCTGTTGTGAGCGAATCAGCCAAGAGCCTGAGGCTGAAGGGAAAAGTACACAGAGGAAGATATTTTACAAACCAGGTCAGTGTA
GGCCAAGACTTATGGTCTACAGATTTTGGCGGGGGAGGGGGGACCTTTTCAAAGACAATAGGGGGTCTTGACATGTTTGTTGTATGTAAAGATGATAAGA
TTAAAATTTTTGATTTTCCTAAAA

Loop counts:

3 nts: 4
4 nts: 1
5 nts: 2
6 nts: 1
7 nts: 2
8 nts: 1

Tetra-loop variants:

GCAA    1

Single bulge variants:

G x 0 bulge: 1
A x 0 bulge: 1
U x 0 bulge: 1
C x 0 bulge: 0

1 x 1 internal loop variants:

G x G bulge: 0
G x A bulge: 0
G x U bulge: 0
G x C bulge: 0
A x G bulge: 0
A x A bulge: 0
A x U bulge: 0
A x C bulge: 0
U x G bulge: 0
U x A bulge: 0
U x U bulge: 0
U x C bulge: 1
C x G bulge: 0
C x A bulge: 0
C x U bulge: 1
C x C bulge: 0