Sequence
atgc intronic sequence ATGC exonic sequence...tcaccttagttctaggtgtattggattcttaggtcacgtacaggatgttgaggtggaagttctttggcatttgtctgtcattttccttgacatatcacagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG
Basic information
species | Physcomitrella patens |
transcript | PP1S25_10V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S25_10V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G33550.2 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------tcaccttagttctaggtgtattg-----gattcttaggtc--acgtacaggatgttgagg----tggaagttctttggcatttgtctgtcattttccttgacata-----tcacagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG
||| | || | |||| | | || ||| | | | || ||| || || | || ||| || | || | | | || | ||| || || || ||||| ||| || |||||||||||||| ||||||||||||||||| ||||| ||| || |||||||| ||||||||| | || |||
gtgagtcagttattagcaactatacatatccagttatcgatatcaaatgttttttgttttttagctcaaaatgttttttaatgtaaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCG
upper sequence: PP1S25_10V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------tcaccttagttcta--ggtgtattggattcttagg---tcacgtacaggatgttgagg-----tggaagttctttggcatttgtctgtcattttccttgacatatca-----cagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG
|| || || || || |||| | | || | | | || |||||| || | || || | || | || | | || || ||| || || || ||||| ||| || |||||||||||||| |||||||||||||| || ||||| ||| ||| ||||| || ||||||||| | || |||
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgaggtggaagttctttggcatttgtctgtcattttccttgacatatcacagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG
ccttgac putative branch site (score: 4)
tcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaccttagttctaggtgtattggattcttaggtcacgtacaggatgttgaggtggaagttctttggcatttgtctgtcattttccttgacatatcacagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA