Sequence
atgc intronic sequence ATGC exonic sequence...nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttcatgctgtgttgttactgaaggctcgtaagttaatttcacctgtctcgcagGAACCAGAAAAGCACGTGTTTCACATTGTCACTGACAAGCTAAATTATGGTGCTATGAAGATGTGGTTTTTGGCAAACCTTCCTGGCGATGCCACCATTG
Basic information
species | Physcomitrella patens |
transcript | PP1S507_8V6.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S507_8V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttcatg-ctgtgttgttactgaaggctcgtaagttaatttcacctgtc-tcgcagGAACCAGAAAAGCACGTGTTTCACATTGTCACTGACAAGCTAAATTATGGTGCTATGAAGATGTGGTTTTTGGCAAACCTTCCTGGCGATGCCACCATTG
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gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA
upper sequence: PP1S507_8V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttcatg-ctgtgttgttactgaaggctcgtaagttaatttcacctgtctcgcagGAACCAGAAAAGCACGTGTTTCACATTGTCACTGACAAGCTAAATTATGGTGCTATGAAGATGTGGTTTTTGGCAAACCTTCCTGGCGATGCCACCATTG
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gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ntttcatgctgtgttgttactgaaggctcgtaagttaatttcacctgtctcgcagGAACCAGAAAAGCACGTGTTTCACATTGTCACTGACAAGCTAAATTATGGTGCTATGAAGATGTGGTTTTTGGCAAACCTTCCTGGCGATGCCACCATTG
agttaat putative branch site (score: 4)
tttcacct CT-rich tract
taagttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntttcatgctgtgttgttactgaaggctcgtaagttaatttcacctgtctcgcagGAACCAGAAAAGCACGTGTTTCACATTGTCACTGACAAGCTAAATTATGGTGCTATGAAGATGTGGTTTTTGGCAAACCTTCCTGGCGATGCCACCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG