Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctaaatttacaatcttgatgtttcaatatacaggaactcctttgttgacaatcatgactttaagctatgttttttgtcttgtagtattaattttatccgaatgtggtttggtttgctgaagctttattcacttgctattgatgcagAACAAAGAGGAGTTAGTGTTGCGTGGTTTCAACTTTTGCGTGATTGATGAAGTTGATTCTATCCTTATCGATGAAGCTCGCACTCCACTCATCATATCCG
Basic information
species | Physcomitrella patens |
transcript | PP1S9_141V6.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S9_141V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtctaaatttacaatcttgatgtttcaatatacaggaactcctttgttgacaatcatgactttaagctatgttttttgtcttgtagtattaattttatccgaatgtggtttggtttgctgaagctttattcacttgctattgatgcagAACAAAGAGGAGTTAGTGTTGCGTGGTTTCAACTTTTGCGTGATTGATGAAGTTGATTCTATCCTTATCGATGAAGCTCGCACTCCACTCATCATATCCG
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----gtcaccaacagtgagcttgg-atttgattatctgagagacaatctagccacggaaagtaattcttgctttattttct-cctttcattattgattgtat--gagtttattttggatgttttt--tctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
upper sequence: PP1S9_141V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtctaaatttacaatcttgatgtttcaatatacaggaactcctttgttgacaatcatgactttaagctatgttttttgtcttgtagtattaattttatccgaatgtggtttggtttgctgaagctttattcacttgctattgatgcagAACAAAGAGGAGTTAGTGTTGCGTGGTTTCAACTTTTGCGTGATTGATGAAGTTGATTCTATCCTTATCGATGAAGCTCGCACTCCACTCATCATATCCG
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-------------------------------------------------------gaaagtaattctt-gctttattttct-cctttcattattgattgtat--gagtttattttggatgttttt--tctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatccgaatgtggtttggtttgctgaagctttattcacttgctattgatgcagAACAAAGAGGAGTTAGTGTTGCGTGGTTTCAACTTTTGCGTGATTGATGAAGTTGATTCTATCCTTATCGATGAAGCTCGCACTCCACTCATCATATCCG
tattgat putative branch site (score: 3)
tttattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctaaatttacaatcttgatgtttcaatatacaggaactcctttgttgacaatcatgactttaagctatgttttttgtcttgtagtattaattttatccgaatgtggtttggtttgctgaagctttattcacttgctattgatgcagAACAAAGAGGAGTTAGTGTTGCGTGGTTTCAACTTTTGCGTGATTGATGAAGTTGATTCTATCCTTATCGATGAAGCTCGCACTCCACTCATCATATCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC