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

AAAGATTCCGAGGTGCAGAAGTTGTCTGAGTGGGTTGGTCGGCGGCAGTCGGGCCAGACCCAGGACTCTGCGACTTTACATCTTTAAATGGATGAGATGG
CTACCACTCAGATTTCCAAAGATGAGCTTGATGAACTCAAAGAGGCCTTTGCAAAAGTTGATCTCAACAGCAACGGATTCATTTGTGACTATGAACTTCA
TGAGCTCTTCAAGGAAGCTAATATGCCATTACCAGGATATAAAGTGAGAGAAATTATTCAGAAACTCATGCTGGATGGTGACAGGAATAAAGATGGGAAA
ATAAGTTTTGACGAATTTGTTTATATTTTTCAAGAGGTAAAAAGTAGTGATATTGCCAAGACCTTCCGCAAAGCAATCAACAGGAAAGAAGGTATTTGTG
CTCTGGGTGGAACTTCAGAGTTGTCCAGCGAAGGAACACAGCATTCTTACTCAGAGGAAGAAAAATATGCTTTTGTTAACTGGATAAACAAAGCTTTGGA
AAATGATCCTGATTGTAGACATGTTATACCAATGAACCCTAACACCGATGACCTGTTCAAAGCTGTTGGTGATGGAATTGTGCTTTGTAAAATGATTAAC
CTTTCAGTTCCTGATACCATTGATGAAAGAGCAATCAACAAGAAGAAACTTACACCCTTCATCATTCAGGAAAACTTGAACTTGGCACTGAACTCTGCTT
CTGCCATTGGGTGTCATGTTGTGAACATTGGTGCAGAAGATTTGAGGGCTGGGAAACCTCATCTGGTTTTGGGACTGCTTTGGCAGATCATTAAGATCGG
TTTGTTCGCTGACATTGAATTAAGCAGGAATGAAGCCTTGGCTGCTTTACTCCGAGATGGTGAGACTTTGGAGGAACTTATGAAATTGTCTCCAGAAGAG
CTTCTGCTTAGATGGGCAAACTTTCATTTGGAAAACTCGGGCTGGCAAAAAATTAACAACTTTAGTGCTGACATCAAGGATTCCAAAGCCTATTTCCATC
TTCTCAATCAAATCGCACCAAAAGGACAAAAGGAAGGTGAACCACGGATAGATATTAACATGTCAGGTTTCAATGAAACAGATGATTTGAAGAGAGCTGA
GAGTATGCTTCAACAAGCAGATAAATTAGGTTGCAGACAGTTTGTTACCCCTGCTGATGTTGTCAGTGGAAACCCCAAACTCAACTTAGCTTTCGTGGCT
AACCTGTTTAATAAATACCCAGCACTAACTAAGCCAGAGAACCAGGATATTGACTGGACTCTATTAGAAGGAGAAACTCGTGAAGAAAGAACCTTCCGTA
ACTGGATGAACTCTCTTGGTGTCAATCCTCACGTAAACCATCTCTATGCTGACCTGCAAGATGCCCTGGTAATCTTACAGTTATATGAACGAATTAAAGT
TCCTGTTGACTGGAGTAAGGTTAATAAACCTCCATACCCGAAACTGGGAGCCAACATGAAAAAGCTAGAAAACTGCAACTATGCTGTTGAATTAGGGAAG
CATCCTGCTAAATTCTCCCTGGTTGGCATTGGAGGGCAAGACCTGAATGATGGGAACCAAACCCTGACTTTAGCTTTAGTCTGGCAGCTGATGAGAAGAT
ATACCCTCAATGTCCTGGAAGATCTTGGAGATGGTCAGAAAGCCAATGACGACATCATTGTGAACTGGGTGAACAGAACGTTGAGTGAAGCTGGAAAATC
AACTTCCATTCAGAGTTTTAAGGACAAGACGATCAGCTCCAGTTTGGCAGTTGTGGATTTAATTGATGCCATCCAGCCAGGCTGTATAAACTATGACCTT
GTGAAGAGTGGCAATCTAACAGAAGATGACAAGCACAATAATGCCAAGTATGCAGTGTCAATGGCTAGAAGAATCGGAGCCAGAGTGTATGCTCTCCCTG
AAGACCTTGTGGAAGTAAAGCCCAAGATGGTCATGACTGTGTTTGCATGTTTGATGGGCAGGGGAATGAAGAGAGTGTAAAATAACCAATCTGAATAAAA
CAGCCATGCTCCCAGGTGCATGATTCGCAGGTCAGCTATTTCCAGGTGAAGTGCTTATGGCTTAAGGAACTCTTGGCCATTCAAAGGACTTTTCATTTTG
ATTAACAGGACTAGCTTATCATGAGAGCCCTCAGGGGAAAGGGTTTAAGAAAAACAACTCCTCTTTCCCATAGTCAGAGTTGAATTTGTCAGGCACGCCT
GAAATGTGCTCATAGCCAAAACATTTTACTCTCTCCTCCTAGAATGCTGCCCTTGACATTTCCCATTGCTGTATGTTATTTCTTGCTCTGTTATCTTTTG
CCCTCTTAGAATGTCCCTCTCTTGGGACTTGCTTAGATGATGGGATATGAATATTATTAGACAGTAATTTTGCTTTCCATCCAGTATGCTAGTTCTTATT
CGAGAACTATGGTCAGAGCGTATTTGGATATGAGTATCCTTTGCTTATCTTTGTAGTACTGAAAATTTGCCGAAGTAACTGGCTGTGCAGAATGTAATAG
AAGCTTTTCTTATTCTTTTATTCTTAAGATCAGTATCTTTTTACAGTATTCTTTCTACATGATCCTTTTTTGTACATTTAAGAATATTTTGATTATATTA
AACAAGACTGCTGATTTTGCTACTTTTTTTAAGGGGTCTTCAAGTAAGTAAAACATACATCGTAGCTAGAAGAAAAATGTACCTTAAATTTGCATCTTCC
CTCTCATACCCAAGCTGTAAACAATTGAAATATTTTGTCTTAAATCACTTGGTTCAATACATGCTTATTTGTTTTAAAACCTGTATCATCAAACTCTCTC
TCTAAATTTAAAATGCTGTTGAATATGATACTTTTGAGGAGAGAGTGTGCTCAGAACTTAGACGGGATTTGGTAGGCCAAGTATGCTAAGTGTACAATAT
ATTTTTTAATTTTACACCTGAAACAAAGAAATGTGGTCACTAAAAATAAAAGTATATATGTAGGAATTAATGTACTCTTGCTTTGTCAAGCTGTTTGCTA
TAGTTTCCAAGGTATTATGTTACTCTAACTCTGAAAAGTGATGTAATCTGGTAGCAATGTAGTAGTTCAAATAAAGGCATTTACATAATAATTAGTCTGT
TCTTCATGCTTTTGTCTCTTAGGAAGTATGCCAATGTTTGTCAGGATTTTTTTCTTTTTGTTTTTCTGATGTATTCTGTAAAATGGTGTTTGTTAAATTT
GAGTTTTGGGAGCTGAATTAGAGGTACTGAATTAAGGACAGTACAAATGAAGTAAAAAGGTTTTCTCCAATTTACCAAAA

Loop counts:

3 nts: 3
4 nts: 10
5 nts: 1
6 nts: 3
7 nts: 1
8 nts: 2
9 nts: 1

Tetra-loop variants:

CAAC    1
UAAC    1
AAAC    1
AUCU    1
GUAU    1
CACG    1
AUUC    1
UGAC    1
UUUG    1
UUCU    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: 1
G x U bulge: 0
G x C bulge: 0
A x G bulge: 1
A x A bulge: 0
A x U bulge: 0
A x C bulge: 1
U x G bulge: 0
U x A bulge: 0
U x U bulge: 1
U x C bulge: 1
C x G bulge: 0
C x A bulge: 1
C x U bulge: 1
C x C bulge: 0