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

TGGTTCCTATCAGCTTCCGTAGCGTCCCTAACGACTTCCGCCTCTGGCGGGCCGCAGTGGTGGAGGAACTTCCGGCAGCGGCAGCTCAAGTGGCCAAGGC
AAGATGGGTCAAAGTCAGAGTGGTGGTCATGGTCCTGGAGGTGGCAAGAAGGATGACAAGGACAAGAAAAAGAAATATGAACCTCCTGTACCAACTAGAG
TGGGGAAAAAGAAGAAGAAAACAAAGGGACCAGATGCTGCCAGCAAACTGCCACTGGTGACACCTCACACTCAGTGCCGGTTAAAATTACTGAAGTTAGA
GAGAATTAAAGACTATCTTCTCATGGAGGAAGAATTCATTAGAAATCAGGAACAAATGAAACCATTAGAAGAAAAGCAAGAGGAGGAAAGATCAAAAGTG
GATGATCTGAGGGGGACCCCGATGTCAGTAGGAACCTTGGAAGAGATCATTGATGACAATCATGCCATCGTGTCTACATCTGTGGGCTCAGAACACTACG
TCAGCATTCTTTCATTTGTAGACAAGGATCTGCTGGAACCTGGCTGCTCGGTCCTGCTCAACCACAAGGTGCATGCCGTGATAGGGGTGCTGATGGATGA
CACGGATCCCCTGGTCACAGTGATGAAGGTAGAAAAGGCCCCCCAGGAGACCTATGCAGATATTGGGGGGTTGGACAACCAAATTCAGGAAATTAAGGAA
TCTGTGGAGCTTCCTCTCACCCATCCTGAATATTATGAAGAGATGGGTATAAAGCCTCCTAAGGGGGTCATTCTCTATGGTCCACCTGGCACAGGTAAAA
CCTTGTTAGCCAAAGCAGTAGCAAACCAAACCTCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTATTCAGAAGTACCTAGGTGATGGGCCCAAACT
CGTACGGGAATTGTTCCGAGTTGCTGAAGAACATGCACCGTCCATCGTGTTTATTGATGAAATTGACGCCATTGGGACAAAAAGATATGACTCCAATTCT
GGTGGTGAGAGAGAAATTCAGCGAACAATGTTGGAACTGCTGAACCAGTTGGATGGATTTGATTCTAGGGGAGATGTGAAAGTTATCATGGCCACAAACC
GAATAGAAACTTTGGATCCAGCACTTATCAGACCAGGCCGCATTGACAGGAAGATTGAGTTCCCCCTGCCTGATGAAAAGACGAAGAAGCGCATCTTTCA
GATTCACACAAGCAGGATGACGCTGGCTGATGATGTAACCCTGGACGACCTGATCATGGCTAAAGATGACCTCTCTGGTGCTGACATCAAGGCAATCTGT
ACAGAAGCTGGTCTGATGGCCTTAAGAGAACGTAGAATGAAAGTAACAAATGAAGACTTCAAAAAATCTAAAGAAAATGTTCTTTATAAGAAACAGGAAG
GCACCCCTGAGGGGCTGTATCTCTAATGAACCATGGCTGTCATCAGGAAAATGGTTGGGAGATTTCTCAATCCCTGAAAGGGATGAGGTTGGGGGAGTTG
CCCAGAGGAATCCCTGTTCCCACTGATTTTTATTAGCAAAACATCCTGTGTCTTTTGGAGTACGATGTGTAAGTGCCCATTGGGTGGCCTGTTGGTCACT
GTGCAGCAGTCTGCTTCCCAATAAAGCGTGCTCTTTCACAAACACTTCCTGTTTCTGCAGTCTCCACACACACCTACCGCTCAACAGCAGCCTGTGGGTG
GACCCAGCTACAGGGAAGCCTTTGGACAGGAACTCAGGCTGCGGTCCCAAGGAGTGTGGACCTCACTATGCGTTCGCCACATCACACCCCCAGAGCTGGC
GTTCAACGGTAATTACAGTGGGAAATGGTCACTACCACAGAGCCAGGGATATTCGTTGTTTAAATAATAAAGGCTGCGTTAATGTGGCTATTGCTTCCAA
AGGAAGTACAGCTTTCCTTTTTGGAAGTTTTGTGGACCATGCATGTTCTTAGCACTCTGAGGGCAGAAAATAACTACTGGTGTTCCCAAGAGACTGAGGA
TTCCTAGAGATATCTTGAAAGCCCTTCTGAGCCCTTGGGCTCAGAAATCTCATCCCTTTCAAGGTGTTCAGAAACATGTCAGAACTTCCCCTTCCCTTTC
TCCGTCTATTTCCGTCATTTCTCTTTCTGAACAAATCAGGCCTAAAGCTATTAAGTGGGACAGATCAAGGTAAGCGTTCCCTTGACAGGTGGCCTGGTGT
GGGTTGTAGGGCCCACACTGAATGAGGAGTGTGTATTAGTTTTCTGTTAATACTATAACAAGTTACCACAGGCTTTGTTTAAAAACAGCACAATTTGGCC
AGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAAGCTGAGGCAGGCGGATCACAAGGTCAGAAGTTTGAGGCCAGCCTGGCCAACATGGTGAA
ACCCCATCTTTACTAAAAATACAAAAATTAGCTGTGCGTGGTGGCAGGTGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGACAATCGCTTGAACC
CAGGAGGCGGAGGTTGCAGTGAGCCAAGATCCCGTCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCCGTCTCAAAAATAAATAAATAAATAAATAA
AAACCACAATTTTATCTCAGTTCTGTAGGTCAGAAGTCCAACACGAGTGTCTCCAGGCTAAAGTCTTGCTGTTGGCAGGACCGTTCCCTCTGGCGTCTCT
AAGGGAGAATCCGTTTCCTTGCTGAGGATTATTGTTGGCAGAATTTAATTTCTTGGAGTTGTGGGCCAGCTGAGGTCAGCATTTCCTTGCTGGCTGCCAG
CTGAGGCCTTTGCCAGTCTGTGAAGGCCACCCTCCCTCCTGACTCGTGGCACTTCATTTTCCACCAGCAGCAGCAGGCCCAGTCCCTCTCTCCCACCGAC
CCTTCTTTCTGCCTGCCTTTTCTATTCTTATGGATCCTTGTGATTGCATTGGACCCATGCAGATGATCCAGGATAATTTCCCTGTTTTAAAGTTTACAAT
CTTCTTAATTTTTATCTGCAAAGTTCCTTTTGCCATGTAACATTCACACGTTCCAGGGCTTAGGGTGTGGCCATCTTTAGGGGCGCCACTCTGCCTACCA
CAGAGGACATCCACACGTGGGGGTGGCCCAGTGCAGGGTAAGGACGGGGTGCTTGTGGGGAGGGCGGGTGTCAGCCCAAGTAGGGTGTGGAGCTGTCCAT
GTGGAGGAACACCACAGCACGGGGACTCAGCATGGGCAGGGTGAGGCTGGCATCCGTGTGGGGTGTATGTGCAGGGCTGGGGTGGTCCGATAGGGGGAGT
CAGTGTGGGCAGCCTGATGTGCAGTATGAGAGCCCAAGTGGGTGAGGAAGGCATCTGCAGGGACGGGGTGGTGGCAGGGGAGGGAGGCTGCTTATGTATG
GAGGCAGTCAGGCAGGTAAACAGGACAGTGGGAGCCAGGTTTCTCTGAGGAGTTAGACACAGAAAGAAGAAAACAAGAACGACCTCTGTCCACTGGGAGC
ACCTGGGAACAGTGACACCCCAACTGCAGTGAGCACCCCTAGACCCAGACCTTTGCTGCTAAAAGTATTATTCTCCACTAAAAGGAGTGAGGGCTGATTC
CGGGGCTAGGCAGGGAAAGGACAGGATGAACCCAAAGTCTGTTTTGCCAGAAAGCAAGGGAGTGCTCAAGGAATGATAAGGACATGTCCTAAGGACACCG
AAGCCTATGTGAAGGGGCTTCCACTGGCCAAACTCGGGACAATCTGAGCATCCTAACAAACAGTTACTATTAATGGAATACAGTATAGCCCTTTAAATAG
GGAACTACACACACACACACACACACACACACACACACACACACACACACACACACACCCCAATACATATGAATTGATCTGAAAGTTTGCTGAGGAAGGG
GTATTTACAGATTTTGAGAGTCTGCCACAAAACACTGTTCAGTTAGAAAGGGAAAGTCACACTGGAGATGCCCAGCAGACACCGTCTTCACCAAGTGGTC
AAATGCACATCATCAGTAATGGGCACTTTGAAAGTACGTGCCACCCAAGAGTGTCAGTGCTGTCACACTCCTGCCAAAGATGCTTAGCCTGAATCCAGTG
CTGAGGAAACACCAGGCAAACACAAACTGAGGAACATTCTACAAATTCAGAACACTTCAAAAGTATCCACGTCTTGGAAGTCAAAAAGCTTCCAATCAGA
AGGAGACCAAAGAGATGACAACCAAGTGCAGCTCCTGCTCCTGAACTGGATCCTTTTCCTAGAGGACATGACTGGGCCTGAGGACCTGCTAGGAGTACTG
CGTCCATGCTGACTTCCTGTTCAGTGTCTGTATCGTGGGCGGGTAGCAGACTCTCAGCAACTGACTCACACGGTTCAGGAAACAAAATTCTTTGTAACGC
ACTTGCATCTTTTCCTAAGTTTGAGATTAAAAAAAACAAAAAACCCCA

Loop counts:

3 nts: 2
4 nts: 2

Tetra-loop variants:

GUGG    1
ACAA    1

Single bulge variants:

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