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

TCAAAAGAAAAAGGGGGAAAAAAAACCATGCAAATTAGATATCTCTGAATTTCTTGCAAATTAAATAAGACGCAGATTCTGGCTCAGGAAAGTGATGCAA
ACGCGTCGTTTTCAAAGGAGAGACCCCAGCCTCGGGTCAGGCGCGGCGCAGACAGCGGCGCGGGGTCCTTGGCTGGGCGGGGCTTGCTCGCGGTGGCTTG
TGGCTCCTTCCTGCGGTGCTTCTCTCTTTCGCTCAGGCCCGTGGCGCCGACAGGATGGGCAAGTGTCGTGGACTTCGTACTGCTAGGAAGCTCCGTAGTC
ACCGACGAGACCAGAAGTGGCATGATAAACAGTATAAGAAAGCTCATTTGGGCACAGCCCTAAAGGCCAACCCTTTTGGAGGTGCTTCTCATGCAAAAGG
AATCGTGCTGGAAAAAGTAGGAGTTGAAGCCAAACAGCCAAATTCTGCCATTAGGAAGTGTGTAAGGGTCCAGCTGATCAAGAATGGCAAGAAAATCACA
GCCTTTGTACCCAATGACGGTTGCTTGAACTTTATTGAGGAAAATGATGAAGTTCTGGTTGCTGGATTTGGTCGCAAAGGTCATGCTGTTGGTGATATTC
CTGGAGTCCGCTTTAAGGTTGTCAAAGTAGCCAATGTTTCTCTTTTGGCCCTATACAAAGGCAAGAAGGAAAGACCAAGATCATAAATATTAATGGTGAA
AACACTGTAGTAATAAATTTTCATATGCCAAAAAATGTTTGTATCTTACTGTCCCCTGTTCTCACCACGAAGATCATGTTCATTACCACCACCACCCCCC
CTTATTTTTTTTATCCTAAACCAGCAAACGCAGGACCTGTACCAATTTTAGGAGACAATAAGACAGGGTTGTTTCAGGATTCTCTAGAGTTAATAACATT
TGTAACCTGGCACAGTTTCCCTCATCCTGTGGAATAAGAAAATGGGATAGATCTGGAATAAATGTGCAGTATTGTAGTATTACTTTAAGAACTTTAAGGG
AACTTCAAAAACTCACTGAAATTCTAGTGAGATACTTTCTTTTTTATTCTTGGTATTTTCCATATCGGGTGCAACACTTCAGTTACCAAATTTCATTGCA
CATAGATTATCTTAGGTACCCTTGGAAATGCACATTCTTGTATCCATCTTACAGGGGCCCAAGATGATAAATAGTAAACTCAAAATTGCTCCCCACTCTG
TTTATTATTTAAAGGTGTCAGGATCTGTGTTGTAATGTGTCTACATTAATGTGTTTAGGAGAATACAGGCATTGGATCATTTAGTTGATGGAAGTATATG
CCAGGCAAGGGAGATAAGGTATACGACAAGACTGATGTTTTCAGTATCTTCTCATGAGGTTGTCAGAGACCTTCATGTCTTCAAAGACTAGTCAGCAAAT
GAAGTGGTTTAGTGTAGAGACAAGATTGGTTGTGTTTTGATAATTTAAGCTAGGTATTGAGTACATGTGGATTTTGCTGTCCACAAATACTTGTTTCAGA
GTTTTCATGGATACAGTGGCATGGTTGAAATGAAGCTGTGAGCCTTCTGCTTTAAATCTGATGTAAGAAACTCCTGTTAACAAATAGTAAGTATGGGTTA
ATTAGCCCTTTGATCAAAGCCTAGCTTTACATTGTTTAGGATCTTTGGAAAACAATTGGTTTGGTTGCCCACTTTCCGTAGGATCAAGAGCAGAACCTTT
CACATGGCACAGAAGAACCCAGGTTGCGCTTCATACCTGCATATTCCAGCCTTAGCCTGCCATTTCTCTCCTTGGCACTTTGTGCTCCAGCAACACTGGT
CTCAGTTGGTCATCCTCAAACTTGGGTTCCATATCCAGCCTCAGGACCTCTGTTCCTGTTACTATGGTTCCTTGCATGTCGCCTGCTCTTACTAAAGAGC
TCGTGTGTTTTCCAGCACACTTCGGTTTATCTCTTGATGATGATGCTAGTCTCTCCCTCCGCAAGGGCGGAAAGGCTGCCTGTTGGTTTGTACCAGTGTT
TCCTAACGTGTAGCTGCAGTCAGTATTTGGCTAAGCTGTTCCCAGGGGCTCAACAGATGCTTTCGGATGAGCCTTAACTGACCCAATCCTTTGTGATGCG
GGAGAGATTGCTAGGCCTCGCTCACCTGGCCAGAACCAGGGAAAGAGGCCGCGGTTGCAGCGCGATTCCAGGCCCTGGGCGTCAGGCGCGGGGTGGGCAG
CTCTCCCCGGGCGGTGGGGCCCTTGTGACCGCGAGGCGGGGCGCACCAGGAAGGGAGTGGGACAGCGCGGGCGCCCAGGGATGTGGCCTGGTTACCTGCC
TTCTCTGATACGTCAAGACACCTTCAACAATGGCTTGCAGCTGTACCCTGTTGGCTGCACCCAGGACGCCCTTTTCACTGCTAAGCAGTCCTACCTGAGG
CCCAGGGGCTGCCAGATTGACCCATAAATAATCTCCGGCGCCTCAGATCCAGAAGCTGCTGAGCCTGATCTTAGTGCCTTCTCCTTTCTCTGTGTGGCCC
CCCAGCCCCTTTCCCCACTGCCTTGTGTCCAAGGCCCTTTCCTTCATGTATCCATGGAGGAGAGACAAAAATACACATCAATAAAATAAGATAGGGAATC
CATAAATAGACATTCAGAAGTATGGCCAACGGATTTATCTTAAAACCAATGGAGGAAGAAGAGTTTCAATAAATGTTGTGGACTTCCATTTGTCAAAGAC
CAAAACAAAGGAACCCCAACCTTACATGTAATACAAACTTAACTCAAAATGGATCATATATCTAAATGTAAAATGGAAAGCTATAAAACTGAAAACAGAC
TATCTTTACAACCTAGGCGTAGGTATAGTTTTTAGACATTACACCAAAAGCACATGCCGTAAAAGAAAAAATAGATAAATTGGTGGATTTCATTAAAATT
AAAAAACTTTTTCTCTCTGAAAAATCCTGTTAAGCTGGGCGCTGTGGTTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGTTGGGAAGAAATTAATA
GCTTGAGGCCAGGAGTTCAAGATCATCCTGGGCAGCAAAGTCATACACTCTTGAGGGAAGAGAGAGACCTTCTCATATTGTTTTATATTGTTTTATACTC
AGTACCTGTTTTAAGAAAAAAACAAGGAAGTGAAATCAAAGACAGGCAGCCCGGCACCAGGCCTGAAACCAGCCCTGGGCCTGCCTGGCCTAAACCTAGT
AGTTAAAAATCAACTTACGACTTAGAACCTGATGTTATCCGTAGATTCCAAGCATTGTATAAAAAAATTGTGAAACTCCCTGTTGTGTTCTGTACCAGTG
CATGAAACCCCTGTCACATATCCCCTAGATTGCTCAATCAATCACGACCCTTTCATGTGAAATCTTTAGTGTTGTGAGCCCTTAAAAGGGACAGAAATTG
TGCACTTGAGGAGCTCAGATTTTAAGGCTGTAGCTTG

Loop counts:

4 nts: 3
7 nts: 1

Tetra-loop variants:

UGCU    1
AAAA    1
GACA    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: 2
U x C bulge: 0
C x G bulge: 0
C x A bulge: 0
C x U bulge: 0
C x C bulge: 0