Sequence
atgc intronic sequence ATGC exonic sequence...nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT
Basic information
species | Physcomitrella patens |
transcript | PP1S1_203V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ16073 (Selaginella moellendorffii), 3'ss of exon 5
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT-----------
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----------------------------------gtagaagctattctcttttctcttttttctgtttttcaatggtgagcaaacttctatgtgc--------------agTATGGCAAGGACTATGACTATGACGCCCCGGTGAAGCTGCTGAACAAGCTTTTGCATTCGATGGCCAAAACTGAAGACGAGCAGCTAGTGGTGGTGTCTC
upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ16952 (Selaginella moellendorffii), 3'ss of exon 5
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT-----------
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----------------------------------gtagaagctattctcttttttcttttttctgtttttcaatggtgagcaagcttctatgtgc--------------agTATGGCAAGGACTATGACTATGACGCCCCGGTGAAGCTGCTGAACAAGCTTTTGCATTCGATGGCCAAAACTCAAGACGAGCAGCTAGTGGTGGTGTCTC
upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ08981 (Selaginella moellendorffii), 3'ss of exon 5
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT-----------
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---------gtaagaaggacctgcgtagtacttgatttccgagacagcctttttcttcccattgaagacactgagtggaagcagctgtgttg---------------gcagTATGGCAAGGACTATGACTACGATGCTCCGGTGAAGTTACTGGATAAGCTCATGCACAACTTTGCACAGACTGAAGACGAGCAGCTAGTTGTCATATCTC
upper sequence: PP1S1_203V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ30037 (Selaginella moellendorffii), 3'ss of exon 5
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT-----------
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----------gtaagaaggacctgcgtagcacttgattccgagacagcctttttcttcccattgaagacactgagtggaagcagctgtgttg---------------gcagTATGGCAAGGACTATGACTACGATGCTCCGGTGAAGTTACTGGATAAGCTCATGCACAACTTTGCACAGACTGAAGACGAGCAGCTAGTTGTCATCTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT
ctgtttt CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactgttttgtgcttgagGGGTGTGGCAGTATGGGAAGGACTATGATTATGATGCTCCTGTGAAACTGCTGGACAAGCTGCTTCATTCAATGTCTCAGTGCGATGACGAGCAACTCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT