Sequence
atgc intronic sequence ATGC exonic sequencegtcgacttttacaccttaatttactctactctgctttccagtactagtgttctttcaacaagtttttagggatttcgggaattgtgatattggtggtggaatttgggatgttttctgattgtaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGACTGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g06410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g33660.1 (Oryza sativa), 3'ss of exon 1
gtcgacttttacaccttaatttactctactctgctttccagtactagtgttctttcaacaagtttttagggatttcgggaattgtgatattggtggtggaatttgggatgttttctgattgtaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGACTGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCAT
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--------------gtgagtttggacagacctgaatttcacc-------ctcttgcaaagaaatgtaggtaaaat-----gctatgaaatt--tagtgagaatttgg------tcaacatattgcagGTTTGCAGAGGTGCGGCAAGAGTTGCAGGTTGCGATGGACAAACTACCTGAGACCAGACATCAAGAGAGGAAAATTCAGCTTACAAGAAGAGCAGACCAT
upper sequence: Vv17s0000g06410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G111117_T01 (Zea mays), 3'ss of exon 1
gtcgacttttacaccttaatttactctactctgctttccagtactagtgttctttcaacaagtttttagggatttcgggaattgtgatattggtggtggaatttgggatgttttctgattgtaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGACTGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCAT
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----------------------------------------gtgagtatggacagacctgaattctctaccatcttccaaatgaacgaagcttgtga--gatctcgagcaacatactg-------cagGCTTGCAGAGGTGTGGGAAGAGCTGCAGGTTGAGGTGGACAAACTACCTGAGGCCGGACATCAAGAGGGGCAAGTTCAGCTTGCAAGAAGAACAGACCAT
upper sequence: Vv17s0000g06410.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S2_55V6.1 (Physcomitrella patens), 3'ss of exon 1
----------gtcgacttttacaccttaatttactctactctgctttccagtactagtgttctttcaacaagttttta--gggatttcgggaattgtgatattggtggtggaatttgggatgttttctgattgta-acagGTCTTCAAAGGTGTGGGAAGAGCTGCAGACTGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCAT
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gtaggcatgaacctcttttttcttctaaaacttcaacaacgtcgtgcatagaagtcatctaagttcggtgatttcacatcggagcggcgcgattgatcgaatt--taatggcgtgtgtg-tatggctggaacatgtgcagGTCTGATGAGGTGTGGCAAGAGCTGTAGATTGAGATGGACGAACTACTTGCGGCCCGACATCAAGCGCGGCCGTTTCTCCGAAGCTGAGGATCAGATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcgggaattgtgatattggtggtggaatttgggatgttttctgattgtaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGACTGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCAT
ttctgat putative branch site (score: 3)
tgatatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgacttttacaccttaatttactctactctgctttccagtactagtgttctttcaacaagtttttagggatttcgggaattgtgatattggtggtggaatttgggatgttttctgattgtaacagGTCTTCAAAGGTGTGGGAAGAGCTGCAGACTGAGATGGACGAACTACCTCAGACCTGATATCAAGAGAGGCAAATTCAGCTTACGGGAAGAGCAGACCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG