Sequence
atgc intronic sequence ATGC exonic sequence...taggtctatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttagagctaaattggtggttgttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
Basic information
species | Physcomitrella patens |
transcript | PP1S69_199V6.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S69_199V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g45300.1 (Oryza sativa), 3'ss of exon 2
taggtctatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttagagctaaattggtggttgttacta--cagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
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--------------gtaagtcataatcacgcattcacgctcattgcctactgtttacctttttaaatctctgtcaaatatgcttatc-ttgccatcatgcagGGAGATGATCCAGCACAGGCCTTATGATCATAAAGTAGATGTTTACAGCTTTGGGATTGTCTTGTGGGAGCTTATAACCGGCATGCTCCCCTTCACAAAC
upper sequence: PP1S69_199V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G31170.1 (Arabidopsis thaliana), 3'ss of exon 3
-taggtc---tatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttaga-gctaaat----tggtggttgttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
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gtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcagAGAGATGATCCAGCACAGACCCTACACTCAAAAAGTGGACGTGTATAGTTTTGGAATCGTGCTGTGGGAGTTGATTACAGGTCTGTTACCGTTCCAGAAC
upper sequence: PP1S69_199V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ13809 (Selaginella moellendorffii), 3'ss of exon 1
taggtctatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttagagctaaattggtggttg---ttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
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---gtaagcgcatttctctcttcgttc------tcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTTTGGCATTGTGCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC
upper sequence: PP1S69_199V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
taggtctatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttagagctaaattggtggttg---ttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
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---gtaagcgcatttctctcttcgttc------tcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaaaaaagccaccttttatattgtttagagctaaattggtggttgttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
agctaaa putative branch site (score: 3)
ttttatattgtttaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggtctatgcattatgaacaagacacaaaaaataaaagagaggaagaaaaaagccaccttttatattgtttagagctaaattggtggttgttactacagGGAGATGATTCAGCACAGACCCTACAATCATAAGGTGGACGTGTACAGCTTTGGCGTTGTTTTGTGGGAGCTTGTGACAGGCCTGTTACCCTTCCAAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT