Sequence
atgc intronic sequence ATGC exonic sequence...tgttatcatctcgtagctactaaacgaatggtattttacttctcactgctatcgagacaacaagctttaaagtgttaaggggtaaactattttaatgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
Basic information
| species | Physcomitrella patens |
| transcript | PP1S88_136V6.1 |
| intron # | 33 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 3'ss of exon 33
lower sequence: GRMZM2G326643_T01 (Zea mays), 3'ss of exon 34
tgttatcatctcgtagctactaaacgaatggtattttacttctcactgctatcgagacaacaagctttaaagtgttaaggggtaaactatttta-atgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
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gtttatttgctgttatctagcca-cacataatacattttttattgatattgccttgccttaacatcttgctctttattttgccgtcctgttatataaatagGAAATATACTGCATTAAATTGCCTGGGAACCCCAAGCTTGGTGAAGGCAAACCTGAGAACCAAAACCATGCCATAATCTTCACTCGAGGAGATGCAGTTC
upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 3'ss of exon 33
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 37
tgttatcatctcgtagctactaaac--gaatggtattttacttctcactgctatcgagacaacaagctttaaagtgttaaggggtaaactattttaatgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
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ttttgctagctttt-gttattgaattagattgccataattgcttaggttgctttcttttacttttgctacctccctttattgaa-gttttttgttgtcgcagGAGATATACTCAGTAAAATTACCTGGAAATCCCAAATTGGGAGAAGGGAAGCCCGAGAATCAAAATCATGCAATTATATTTACGCGTGGAAATGCAGTCC
upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 3'ss of exon 33
lower sequence: GLYMA10G44150.2 (Glycine max), 3'ss of exon 35
tgttatcatctcgtagctactaaacgaatggtattttacttctcac----tgctatcgagacaacaagctttaaag--tgtta----aggggtaaactattttaat---gcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
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-------------taattgcttaggttgctttcttttacttttcctacctctctattgaattagatagctttgatatttgtcactccatttgtaagttttttttatctcacagGAGATATACTCGGTGAAGTTGCCTGGAAATCCCAAATTGGGTGAAGGGAAGCCCGAGAATCAAAATCATGCAATTGTATTTACGCGTGGAAATGCAGTCC
upper sequence: PP1S88_136V6.1 (Physcomitrella patens), 3'ss of exon 33
lower sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 35
---------------------------------------------------------------tgttatcatctcgtagctactaaacgaatggtatt-ttacttctcactgctatcgagacaacaagctttaaagtgttaaggggtaaactattttaatgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
||| | | | | | | | || || | || || | | | | || | | || | | |||| | ||||| | ||||| ||||| || |||||||| ||| ||||||||||| || || ||||||||||||||||| || | || ||||| ||||| ||||
gtatatgatattttgtggatacttggaatggttaatttgtcaaattggttttagatacctaaatgtgccaaaatagaaagtttttcctggtctaaatagttggtactttcttcaagtggattgatgagatacatagcacacaataactttcacttttgctatagGAAATTTATTCAATTAAACTTCCCGGAGATCCTAAACTTGGTGAAGGGAAGCCTGAGAATCAAAATCATGCTATCGTGTTTACGCGGGGAGAAGCTATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctatcgagacaacaagctttaaagtgttaaggggtaaactattttaatgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
ttttaat putative branch site (score: 3)
ctatttt CT-rich tract
taaactattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttatcatctcgtagctactaaacgaatggtattttacttctcactgctatcgagacaacaagctttaaagtgttaaggggtaaactattttaatgcagGAAGTATATTCCATTAAGCTCCCCGGAGACGTTAAGCTTGGTGAAGGAAAACCCGAGAATCAAAATCATGCAATAATTTTCACGCGTGGAGATTGCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
