Sequence
atgc intronic sequence ATGC exonic sequence...tggttgctgtgtttaaattaattacttcagacactgcatgggcattttttatatgcatctgacttgtttcattcaatgttttcatccatgacttctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G462803_T02 (Zea mays), 3'ss of exon 17
tggttgctgtgtttaaattaattacttcagacactgcatgggcattttttatatgcatctgacttgtttcattcaatgtt-ttcatccatgacttctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
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tcttgcctatgaaggcatccacaacaagtctatttttttgaaacataattacatggttgt-actgctctcactagtcactacttactcttttgtcttttagGCGAAAGGTTATAGAGTTGGTCCTGTGTATGATGATGTGTTGGCAATGGCTTGGTTTTTTCTGGAGCTTATTGTAAAATCAATGGGATTGGAACAAAGTC
upper sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------------------tggttgctgtgtttaaa-ttaatta--cttca-gacactgcatgggcattt--tttatatgcatctgact-tgtttcattcaatgttttcatccatgact---tctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
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gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC
upper sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: PP1S59_25V6.1 (Physcomitrella patens), 3'ss of exon 19
-----------tggttgctgtgtttaaattaattacttcagacactgcatgggcattttttatatgcatctgacttgtttcattcaatgttttca---tccatgacttctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
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gtaactatttccattatctcgattgaagtttaatctttgttagacagtcggctaggtttctgaatcaatcaactctctctgaaacaggagtttcaatatatgtaacttgtgcagGCGAAAGGCTACCGTGTCGGACCTGTGTATGATGATGTTCTTTCCATGGCTTGGGTGTTCCTGGAGCTAATTGTCAAGTCCATGGCACTTGAACAATCCC
upper sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
tggttgctgtgtttaa--atta--attacttcagacactgcatgggcattttttatatgcatctgacttgtttcattcaatgttttcatccatgacttc-tgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
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---gtacgaagatcaagcattgggatctttttaaat-ttacgaggaaattatttaaatc-------cttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatatgcatctgacttgtttcattcaatgttttcatccatgacttctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
atctgac putative branch site (score: 3)
cttctgc putative PPT
aatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggttgctgtgtttaaattaattacttcagacactgcatgggcattttttatatgcatctgacttgtttcattcaatgttttcatccatgacttctgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
tggttgc
- - - - - - - aaattaa
- - - - - - - - - - - - - - - -cactgca
- - - - - - - - - - - - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcaa