Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcctgcattctcctacctcacaaacattcatgtccgctattacgtattttggtgttttctgaaggactttcgattaacccaactcccctacgttcgatttctcttgtttcgtggaacatccacaactatgttaggacgctccgatctgaacgtaacctacatttggtgatgcagCTAGATGATTGGGTCCTGTGCCGAATTTATGAAAAAACCACCCATGCCCAGCGAGCTGGAAAGGAACAGGAAAATTCCTGCGTCGAGGAGGTGTTAGCGT
Basic information
species | Physcomitrella patens |
transcript | PP1S15_200V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S15_200V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
gtatgtcctgcattctcctacctcacaaacattcatgtccgctattacgtattttggtgttttctgaaggactttcgattaacccaactcccctacgttcgatttctcttgtttcgtggaacatccacaactatgttaggacgctccgatctgaacgtaacctacatttggtgatgcagCTAGATGATTGGGTCCTGTGCCGAATTTATGAAAAAACCACCCATGCCCAG----CGAGCTGGAAAGGAACAGGAAAATTCCTGCGT-CGAGGAGGTGTTAGCGT
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--------------------------------------------------------------------------ttaattgggcggatttcatcatatatttattgttgtgat-cacgaaatgat-atggtcttgatgaaa---tttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCGGCGGCGGCGAACGTTCGAATATGATGAGCCACG-----
upper sequence: PP1S15_200V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0014g03290.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtcctgcattctcctacctcacaaacattcatgtccgctattacgtattttggtgttttctgaaggactttcgattaacccaactcccctacgttcgatttctcttgtttcgtggaacatccacaactatgttaggacgctc--cgatct-gaacgtaacctacatttggtgatgcagCTAGATGATTGGGTCCTGTGCCGAATTTATGAAAAAACCACCCATGCCCAGCGAGCTGGAAAGGAACAGGAAAATTCCTGCGTCGAGGAGGTGTTAGCGT-----
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--------------------------------------------------------gtagatattaaat-attatcagttaaaccaaaaac------ttaaattttttcagtactaaacaataatatcaagtacaattg-acgcttaacaatctcgtatctgggtttcttgttttgatgcagTTGGATGATTGGGTTCTGTGCCGAATTTACAAGAAGAATTCCAACTCTTCGAAACCCATAG-----CAGCTGTACTTCCCAGCAAAGCGCACAGCAACGGCTCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccacaactatgttaggacgctccgatctgaacgtaacctacatttggtgatgcagCTAGATGATTGGGTCCTGTGCCGAATTTATGAAAAAACCACCCATGCCCAGCGAGCTGGAAAGGAACAGGAAAATTCCTGCGTCGAGGAGGTGTTAGCGT
acgtaac putative branch site (score: 3)
tatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcctgcattctcctacctcacaaacattcatgtccgctattacgtattttggtgttttctgaaggactttcgattaacccaactcccctacgttcgatttctcttgtttcgtggaacatccacaactatgttaggacgctccgatctgaacgtaacctacatttggtgatgcagCTAGATGATTGGGTCCTGTGCCGAATTTATGAAAAAACCACCCATGCCCAGCGAGCTGGAAAGGAACAGGAAAATTCCTGCGTCGAGGAGGTGTTAGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG