Sequence
atgc intronic sequence ATGC exonic sequencegtgcgaatattttccttccttcctgtgcctgagctttggctttttattttttaatttttttatctcattttacatgcgtctcccgtgggattatactcactctagctgtattgccattgaaagcaccaaagttttgatgagccctgcatgtttctccgtgtttgtggcacagCCGAGACGCAGTGATTTGGACATGAACCAGCATGTGAATAATGTGAAGTACATTGGTTGGATGTTGGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S433_34V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S433_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 5
gtgcgaatattttccttccttcctgtgcctgagctttggctttttattttttaatttttttatctcattttacatgcgtctcccgtgggattatactcactctagctgtattgccattgaaagcaccaaagttttgatgagccctgcatgtttctccgtgtttgtggcacagCCGAGACGCAGTGATTTGGACATGAACCAGCATGTGAATAATGTGAAGTACATTGGTTGGATGTTGGAG
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-----------------------------------------------------------gtaagtcagttaatat-tgcttgttaccgt----cattcattttgctggtggttctcatg----cataaaatttctcatgagggatcc---tttgttcatgt--------cagCCGAAGTGGAGTGACCTTGATGTCAACCAGCATGTGAACAATGTGAAGTATATTGGTTGGATACTTGAG
upper sequence: PP1S433_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgcgaatattttccttccttcctgtgcctgagctttggctttttattttttaatttttttatctcattttacatgcgtctcccgtgggattatactcactctagctgtattgccattgaaagcaccaaagttttgatgagccctgcatgtttctccgtgtttgtggc--acagCCGAGACGCAGTGATTTGGACATGAACCAGCATGTGAATAATGTGAAGTACATTGGTTGGATGTTGGAG-------------------------------
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------------------------------------------------------------------------------------gtaagtatctagtatttactgctgtatgtttcaacaaacctttgaccagcttgtaagactctctaatggcttggtaatgaacattttcagCCTCGATGGAGTGACCTAGATGTTAACCAGCATGTGAATAATGTAAAGTACATTGGGTGGATCCTGGAGAGTGCTCCAGTGGGAATAATGGAGAGGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaagcaccaaagttttgatgagccctgcatgtttctccgtgtttgtggcacagCCGAGACGCAGTGATTTGGACATGAACCAGCATGTGAATAATGTGAAGTACATTGGTTGGATGTTGGAG
ttttgat putative branch site (score: 4)
aaagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgaatattttccttccttcctgtgcctgagctttggctttttattttttaatttttttatctcattttacatgcgtctcccgtgggattatactcactctagctgtattgccattgaaagcaccaaagttttgatgagccctgcatgtttctccgtgtttgtggcacagCCGAGACGCAGTGATTTGGACATGAACCAGCATGTGAATAATGTGAAGTACATTGGTTGGATGTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG