Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatttctgactctagcactgttatttattgacatgatcgttgctatgtcgtgcaatggtattcaaggttgtccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaagaaatactccatagtgaataaattcattcatgtttgatggtgaattgaatcttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
Basic information
species | Physcomitrella patens |
transcript | PP1S88_103V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S88_103V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G017334_T01 (Zea mays), 3'ss of exon 4
gtaagcatttctgactctagcactgttatttattgacatgatcgttgctat--gtcgtgcaatgg--tattcaaggttgt-ccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaa--gaaatactccatagtgaataaattcattcatgtttgatggtgaattgaat-cttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
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------gtatgtgcttccagaaa-actattcatttgcatt-tctttcctatcattccagctattgattcttttaggtcgtatcagacccactatattgcatttcttctgctaatagaagtggagttgttagttgtaacattcattgttaacttgcccaaattattctacatttccttttaattattccagATGGGTCTAATGAGGAAACATCCTTCGATCATACCTTTCATGATCTACATCTCTAATGAGGGTAAGCACACAGAGAGGTTTGCTGTACGTGCAAAGTACA
upper sequence: PP1S88_103V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G048553_T02 (Zea mays), 3'ss of exon 4
gtaagcatttctgactctagcactgttatttattgacatgatcgttgctatgtcgtgcaatggtattcaaggttgtccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaagaaatactccatagtgaataaattca-ttcatgtttgatggtgaattgaat-cttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
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-------------------------------------------------------------------------agagccactatattgcatttgttttgctaa--taaaggtggag---ttgtaac------tttcattgtttacatgcccactttattccacatttcgttttaattatttcagATGGGTCTAATGAGGAAACATCCTTCGATAATACCTTTCATGATCTACATATCTAATGAGAGTAAGCACACAGAGAGGTTTGCTGTACGTGCGAAGTACA
upper sequence: PP1S88_103V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv06s0061g00280.t01 (Vitis vinifera), 3'ss of exon 5
gtaagcatttctgactctagcactgttatttattgacatgatcgttgctatgtcgtgcaatggtattcaaggttgtccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaagaaatactccatagtgaataaattcattcatgtttgatggtgaattgaatcttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
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--------------------------------------------------------------------gtaagtgtcttcactaattctaattttttt-----------tttccttctcctgacaaggaatcttt--tagtgttttgttt---ttagttacaatggttgttccaattggcagATGGGGCTTATGAAGAAACATCCGTCAATCATACCATTCATGATATACATCACAAATGAAGACAAACACTTGGAACGATTTGCTGTTCGTGCAAAGTATA
upper sequence: PP1S88_103V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcatttctgactctagcactgttatttattgacatgatcgttgctatgtcgtgcaatggtattcaaggttgtccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaagaaatactccatagtgaataaattcattcatgtttgatggt-----gaattgaatcttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
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---------------------------------------------------------------------------------ccttttat--ttataagatcttctaaactat---gcacaaaaagagaatatttttcttgtaaattgctt-agtgatactaaaaggttctttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatactccatagtgaataaattcattcatgtttgatggtgaattgaatcttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
gtttgat putative branch site (score: 5)
tcttc putative PPT
aataaattcattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatttctgactctagcactgttatttattgacatgatcgttgctatgtcgtgcaatggtattcaaggttgtccaactctatcatggttgtcttacacacctgaatgtccagcactcgcaaagaaatactccatagtgaataaattcattcatgtttgatggtgaattgaatcttcagATGGGTCTCATGAAAAAGCATCCATCAATCATACCGTTCATGATGTACATCGCTAACGAAAGCAAACACATGGAGAGGTTTGCAGTTCGTGCAAAGTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG