Sequence
atgc intronic sequence ATGC exonic sequence...ttatttatttattttttttacatcaacctgttgcagatttttgaaactgaaaacgggttaaagttttcctgaagccttacttttgtgtcgtgaaatgcagGGGCACCCATTGCAGGATCTGCAATTGATGAAGTGAAGGAGGTTGTAGGCTACGTAGCTTTGGGTTATCCTTTTGGAATGTTAGCCTCCGTCCTGTTCGG
Basic information
species | Physcomitrella patens |
transcript | PP1S97_81V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S97_81V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G024211_T01 (Zea mays), 3'ss of exon 1
----ttatttatttattttttttacatcaacctgttgcagatttt-tgaaactgaaaacgggttaaagttttcctgaagccttacttttgtgtcgtgaaatgcagGGGCACCCATTGCAGGATCTGCAATTGATGAAGTGAAGGAGGTTGTAGGCTACGTAGCTTTGGGTTATCCTTTTGGAATGTTAGCCTCCGTCCTGTTCGG
||| | | || | | | | || | | | ||| |||| |||| | ||| || | || || | | | ||| |||||||||||| ||||| ||||||||| ||||| ||||| | || || | || ||||| | || || || ||||| || | ||||| ||||| |||||
agaattaagatgtggtattctgcatacaagtcttctcctgtctttatgaagctga---tgtgttgtgtttaggcatgtatctaacaataattccttga--tgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgaaaacgggttaaagttttcctgaagccttacttttgtgtcgtgaaatgcagGGGCACCCATTGCAGGATCTGCAATTGATGAAGTGAAGGAGGTTGTAGGCTACGTAGCTTTGGGTTATCCTTTTGGAATGTTAGCCTCCGTCCTGTTCGG
gccttac putative branch site (score: 3)
ttaaagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatttatttattttttttacatcaacctgttgcagatttttgaaactgaaaacgggttaaagttttcctgaagccttacttttgtgtcgtgaaatgcagGGGCACCCATTGCAGGATCTGCAATTGATGAAGTGAAGGAGGTTGTAGGCTACGTAGCTTTGGGTTATCCTTTTGGAATGTTAGCCTCCGTCCTGTTCGG
- - - - - - - - - - - - - - tgttgca