Sequence
atgc intronic sequence ATGC exonic sequence...gtccactggtaaagttgattcatccttgatcgtattgcttctgtggctcaatggctgctgcgttgtctgacataggggatttctgggttatggtacacagTACTTGGACGAGAATAAACAGCTGATTCTCGCCATTCTCGACAACCAAAACCTCGGCAAGCTCAATGAGTGTGCGAC
Basic information
species | Physcomitrella patens |
transcript | PP1S158_124V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S158_124V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G180246_T01 (Zea mays), 3'ss of exon 1
----gtccactggtaaa-gttgattcatccttgatcgtattgcttctgtggctcaatggctgctgcgttgtctgacataggggatttctgggttatggtacacagTACTTGGACGAGAATAAACAGCTGATTCTCGCCATTCTCGACAACCAAAACCTCGGCAAGCTCAATGAGTGTGCGAC-
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gggtgagagaaagtaaatgctcagtcaacggtggatacaaagcgtctacactggaatg-----tgacatacttaacaatacgtttttgatcatgaaactgtgcagTACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCG-AACG
upper sequence: PP1S158_124V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ18273 (Selaginella moellendorffii), 3'ss of exon 1
---gtccactggtaaagttgattcatccttgatcgtattgcttctgtggctcaatggctgctgcgttgtctgacataggggatttctgggttatggtac-acagTACTTGGACGAGAATAAACAGCTGATTCTCGCCATTCTCGACAACCAAAACCTCGGCAAGCTCAATGAGTGTGCGAC
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tttgggttttaggagaggagcataaagtgatctctcacagttttgtaaggccaaagctcact---tttttttgctcttttctcttttggatt-tggtgctgcagTACTTGGACGAGAACAAGCAGCTCATACTTGCAATCCTTGACAACCAGAACCTCGGCAAGCTTAATGAATGCGCGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcaatggctgctgcgttgtctgacataggggatttctgggttatggtacacagTACTTGGACGAGAATAAACAGCTGATTCTCGCCATTCTCGACAACCAAAACCTCGGCAAGCTCAATGAGTGTGCGAC
gtctgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccactggtaaagttgattcatccttgatcgtattgcttctgtggctcaatggctgctgcgttgtctgacataggggatttctgggttatggtacacagTACTTGGACGAGAATAAACAGCTGATTCTCGCCATTCTCGACAACCAAAACCTCGGCAAGCTCAATGAGTGTGCGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA