Annotated gene sequence

Experiment = in vitro 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

GGGAGGGCGAACTGCAAGAGGGCTGCCAGGATTAGCCGAGGGATTCCGAATGAAGACGGAGTATTTCCGAACATACACACCTCTCCCAAGAGCGTTTCCG
GAGGGTTCCGAAAATACCCGAGCGGGCCTCGGCGCCCTCATTGGCCATCACCGCGAGGGCTTACGAAGACCGGAAATATCCAAAGGTGCCGGGGCTAGGC
TTATATAGTTCACGCATTCACCAGTTCATTCATAAAACAAATGTTTGTTGAGCGCCCATCATATGCCAATCACAGTGACAAGTGCTGGGTGAGCAATACT
GGAGAGATAACGCTGAGGTATGGGTCCCAGGACCTCTCGAATTGGAGCCACTCGGAAATCCAGCGGTAGAGTTTCGAAAACTTCCGAACGGTTCCCGGAA
TACGCTCTCGGCCCTCTAACCGAAGAGTTCCGAATATTCCCGAGCGTTGAGCGAATTTTCGGCGGAAGCAGCCGAACATCATCGAGCCGCCTCGGAGGTG
GGGACCGACAACTCCTGTCGTGCCCGCCCGGAGAGGAAGCGGAAATGCGTGTACGGTATTAAAGGCGTCGCCTCGCCCCTCGCCTTCCTCTTTCCGTCTC
AGGTCGCCGCTGCGAAGGGAGCCGCCGCCATGTCTGCGCATCTGCAATGGATGGTCGTGCGGAACTGCTCCAGTTTCCTGATCAAGAGGAATAAGCAGAC
CTACAGCACTGAGCCCAATAACTTGAAGGCCCGCAATTCCTTCCGCTACAACGGACTGATTCACCGCAAGACTGTGGGCGTGGAGCCGGCAGCCGACGGC
AAAGGTGTCGTGGTGGTCATTAAGCGGAGATCCGGCCAGCGGAAGCCTGCCACCTCCTATGTGCGGACCACCATCAACAAGAATGCTCGCGCCACGCTCA
GCAGCATCAGACACATGATCCGCAAGAACAAGTACCGCCCCGACCTGCGCATGGCAGCCATCCGCAGGGCCAGCGCCATCCTGCGCAGCCAGAAGCCTGT
GATGGTGAAGAGGAAGCGGACCCGCCCCACCAAGAGCTCCTGAGCCCCCTGCCCCCAGAGCAATAAAGTCAGCTGGCTTTCTCACCTGCCTCGACTGGGC
CTCCCTTTTTGAAACGCTCTGGGGAGCTCTGGCCCTGTGTGTTGTCATTCAGGCCATGTCATCAAAACTCTGCATGTCACCTTGTCCATCTGGAGGTGAT
GTCAATGGCTGGCCATGCAGGAGGGGTGGGGTAGCTGCCTTGTCCCTGGTGAGGGCAAGGGTCACTGTCTTCACAGAAAAAGTTTGCTGACTTGTGATTG
AGACCTACTGTCCCATTGTGAGGTGGCCTGAAGAATCCCAGCTGGGGCAGTGGCTTCCATTCAGAAGAAGAAAGGCCTTTTCTAGCCCAGAAGGGTGCAG
GCTGAGGGCTGGGCCCTGGGCCCTGGTGCTGTAGCACGGTTTGGGGACTTGGGGTGTTCCCAAGACCTGGGGGACGACAGACATCACGGGAGGAAGATGA
GATGACTTTTGCATCCAGGGAGTGGGTGCAGCCACATTTGGAGGGGATGGGCTTTACTTGATGCAACCTCATCTCTGAGATGGGCAACTTGGTGGGTGGT
GGCTTATAACTGTAAGGGAGATGGCAGCCCCAGGGTACAGCCAGCAGGCATTGAGCAGCCTTAGCATTGTCCCCCTACTCCCGTCCTCCAGGTGTCCCCA
TCCCTCCCCTGTCTCTTTGAGCTGGCTCTTGTCACTTAGGTCTCATCTCAGTGGCCGCTCCTGGGCCACCCTGTCACCCAAGCTTTCCTGATTGCCCAGC
CCTCTTGTTTCCTTTGGCCTGTTTGCTCCCTAGTGTTTATTACAGCTTGTGAGGCCAGGAGTTTGAGACCATCCTAGGCAACATAATGAGACACCGTCTC
TAAAATAAAATTAGCTGGGTGTGGTGGTGCACCGCCTGTGGTCCCAGCTCCTCAGAGGTTGAGTAGAGGCTGAGGTGAGCGGAGCACTTGAGCCAAGAGT
ATGAGGCTGCAGTGAGCCCATGAGCCCCACCACTACACTCCAGCCTGGAAGACACCATGACACACAGTGAGGCCTGGATGGGGAAAGAGTCCTGCTGTTG
ATCCTCACATGTTTCCTGGGCACCTAACTCTGTCAGCCACTGCCAGGGACCAAGGATCCAGCATCCATGGCACCCCTGGTTCCTGCCATCCTGGGGTACC
CGATTCAAAGAAGGACTCTGCTCCCTGTCTGAGACCACCCCCGGCTCTGACTGAGAGTAAGGGGACTGTCAGGGCCTCGACTTGCCATTGGTTGGGGTCG
TACGGGGCTGGGAGCCCTGCGTTTTGAGGCAGACCACTGCCCTTCCGACCTCAGTCCTGTCTGCTCCAGTCTTGCCCAGCTCGAAGGAGAGCAGATCTGA
CCACTTGCCAGCCCCTGTCTGCTGTGAATTACCATTTCCTTTGTCCTTCCCTTAGTTGGGTCTATTAGCTCAGATTGAGAGGTGTTGCCTTAAAACTGAG
TTGGGTGACTTGGTACCTGCTCAGGACCCCCCGCACTGTCCCAATCCCACTCAGGCCCACCTCCAGCTGGCCTCACTCCGCTGGTGACTTCGTACCTGCT
CAGGAGCCCCCACTGTCCCAGTCCCACTCAGGCCCATCTCTGGCTGGCCTCACTGCGCTGGGACTCCGCCTTCATAAGGAGAGCTCACTGCTCACGTTAG
TAGATGGCCCCTTCTCGTGAGGCCTCTCCCCTGGCACCTGCTTCAGTTGTCCTCCACAGCACTGATTTGCAGCCCACAAGCTGGCAGGTTTATCTGTCTC
ATGTTTGTCTTGTGCTGGTGGGCAAGGGGTTTGTCTAGCACACCAGCATATAATGAGATGCTTGATGAATGGTGCATATTGAATGTATAAAGCCCACCGG
TCCTGAGAGTTTGCTCACTGGAGACTTTCTGGAGATGGAGTCTCGCTCTGTTGCCCAGGCTGGCGAGTGCAATGGCGCGATCTTGGCTCACTGCAGCCTC
CACCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGTGGGTGTCACCACACCCAGCTCAGTATTGTATTTTTAGCAG
AGATGGGGTTTCACCATTTTGCCCAGGCTGGTTTGGAACTCCTGACTTCAAATTACCCACCTGCCTCAGCCTCCCAAAGTGCTGGCATTACAGGCGCTCG
AGGCTTTCTGATGTGGCTGCTGCTGCTCAGAAGGCCTTGTCCTTAACCACCTCCTTGCCTGCCCTGGAGGCTTGTGCCTCTAGGCCCCACCCCCTGTGGA
GTCCTGCTGGCTTTCTCCATCCCTATCTGAATCCTCCCTGCTGTGTGGCCTCCCCTGGTCTCATCCGTAACACAGCCCAGCTTAGTGGGCCTCTGTTCCT
GCGGGTGGCCAGCCTGTCTGTGTGGCTGGGCTGGGGAGGCCACGTCTGGTATCTGAATGCTATCGGTGGGTTGGGGTGGAGGAACCAGGAGAGGGCTGGA
GGGAGGGAGATGGTCTCAGCCCCACAGAGTTTGGAGTCCTCAGTGTGCTGAGCAAACGTGGAGACACCATTTCCCTCCTCTAGACCTCATCTTGGAGAGA
GAGATGTTGGATGGGGCCATCTATTCCAGCTTTATTCACACAAATCATGTCTGTTGGCCTGGAAATTGGAAAACCAGTTAAACCAAAAACATGATATTAA
GAAAACAGGCAGGCTCACCATAGTAAAAATGCTGAAAGCCAAAGACAAAATTGGGAGAACAAAAGAAAAGCGTCTTGTCACATACAGAAGGTCCCTGATA
AAGTTAGTAGCTGCCCTCATCAGAAACCAGGCCCAGGCAGTGGGGACACATCCAGAGTGCTGAAAGAACCTCCCCCAGGTCATCCTATCCCCAAGAGTGA
TGCCCGGCAGCATTCCCAGCTCAGGGCTAATGGTTCACGGAAGCCAGGAATCAAACTGCCTGGGTTCCAGTCCCAGCTCTGCCAGTTATGCCCAGCTGTG
GGGACTTGGGCAGCTCGTTTAGTAGCACCGTGCCTCAGTTTCCCATATGTAAAAGGCCATTTTGAGTGCCTTTCACAGCCCTGCATAAGGCAGGTGTCTC
AGTGTTCACTGCTGTCTCTCCAGCTCTTAGTCCAGTAGCTGCATGGTGAGTGAGCGTAGGGCGCACCCTGGAAGGCTGCCAAGCCCAAAGTTGTGCAGAG
CGCTGGGGACTCCAGACTCCCCACAGCAGCAGAGACTCGGGACTGAGGCATCCTCTGTTCACAGGACATGCTGGCATCTACTGGGTCAGGGCTCTGCTGC
TCGGTGGCTGTGCAACCTTGGGCAAGTTCCTCAACCTCTCTGTGTCTTCGTACCCTCATCTGTAACATGCGTGTCGATAGACCCTACTACTCAGGGTTGA
TGAGAAGATTAAATGTGCAAAACCTGCTTGACTGTGCCCACAAATCCTGATTGTAGGAATAAATTAATGACTTTTTATAAATATTTTGATCAGATGGACT
CATGATCACAGATGTCTTCACATGCCTATGACTAATTTGTACACAAACTAATGCTCGTGTTTCCCAAGCACCTGGAAGACATGCCAGATCCATGTGCAGT
AATGCCTGGTGGCTCCAGGTCTGCCCCGCCGTCCTGTGGGGCTGTGAGCTTTCCCAGCCTCCTGCCCGTGTTTGTGAATATCATTCTGTCCTCAGCTGCA
TTTCCAGCCCAGGCTGTTTGGCGCTGCCCAGGAATGGTATCAATTCCCCTGTTTCTCTTGTAGCCAGTTACTAGAATAAAATCATCTACTTTAAAA

Loop counts:

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

Tetra-loop variants:

CGCU    1
CAUC    1

Single bulge variants:

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