Sequence
atgc intronic sequence ATGC exonic sequence...ttgatgatgcaatgagtttaatcgcacgtatagatgactcgctgggagaattctcactgaaaagttaaatgtggatgttttcccatccgggataatgcagACAAGGCATTATTCGGGGAGAGAGAGTGGTATTTCTTTTCGCCAAGGGACAGGAAGTACCCCAATGGCGCAAGGCCCAACAGAGCCGCCGCAAGCGGCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S259_83V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S259_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G34990.1 (Glycine max), 3'ss of exon 1
-----------------------ttgatgatgcaatgagtttaatcg-cacgtataga---tgactcgctgggagaattctcactgaaaagtta--aatgtggatgttttc------ccatccgggataatgcagACAAGGCATTATTCGGGGAGAGAGAGTGGTATTTCTTTTCGCCAAGGGACAGGAAGTACCCCAATGGCGCAAGGCCCAACAGAGCCGCCGCAAGCGGCTA
| || ||| || || | ||||| | | | | | | | | | | | ||| | | || | || | | | | | | ||| ||||| || |||||| ||||||||||||||| | || |||||||||||||| || || ||||| ||||| ||||| || ||| || || ||
gtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggtta-acagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACAGGAAGTATCCGAACGGCGCGAGGCCAAACAGGGCGGCCACATCAGGGTA
upper sequence: PP1S259_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G35560.1 (Glycine max), 3'ss of exon 1
------------------------------------------ttgatgatgcaatgagtttaatcg-cacgtatagatgactcgctgggagaattctcactgaaaagttaaatgtggatgttttcccatccgggataat--gcagACAAGGCATTATTCGGGGAGAGAGAGTGGTATTTCTTTTCGCCAAGGGACAGGAAGTACCCCAATGGCGCAAGGCCCAACAGAGCCGCCGCAAGCGGCTA
|| | | | || | | ||| | || | | | | | | ||| | | | ||| | || | || | | | | | |||| ||||| || |||||| ||||||||||||||| | || |||||||||||||| || || ||||| ||||| ||||| || || || || ||
gtatgttcttcaatttcatccaacgaatcaaaagattcaaactttacgttcaaa--actcaaatgggtttgttttactttttattttgtattatttactttttgtatttat-tatgatttttctttatttttgtgtggttggcagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACTCCGAGGGACAGGAAGTATCCGAACGGCGCGAGGCCAAACAGGGCGGCGACATCTGGGTA
upper sequence: PP1S259_83V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA20G04400.1 (Glycine max), 3'ss of exon 1
ttgatgatgcaatgagtttaatcgcacgtatagatgactcgctgggagaattctcac-tgaaaagttaaatgtggatgttttcccatc-cgggataatgcagACAAGGCATTATTCGGGGAGAGAGAGTGGTATTTCTTTTCGCCAAGGGACAGGAAGTACCCCAATGGCGCAAGGCCCAACAGAGCCGCCGCAAGCGGCTA
| ||| | | || || | | || | || | | | | | | | || |||| | || | |||||||| || || ||| || || | || |||||||||||| | ||||| |||||||||||||| ||||| | ||||| ||| |||| ||| || ||
cagctgaaattgtagttgcaaattgttttaaaaac--cttgacatgaatggtattatattacatctctaacacacttgttattaaattaccatggaatgcagATAAAACAGAATTTGGAGAAAATGAATGGTATTTCTTTACTCCAAGAGACAGGAAGTACCCAAATGGGGTGAGGCCTAACCGAGCAACCGTGTCAGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagaattctcactgaaaagttaaatgtggatgttttcccatccgggataatgcagACAAGGCATTATTCGGGGAGAGAGAGTGGTATTTCTTTTCGCCAAGGGACAGGAAGTACCCCAATGGCGCAAGGCCCAACAGAGCCGCCGCAAGCGGCTA
ttctcac putative branch site (score: 2)
aaaagttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgatgatgcaatgagtttaatcgcacgtatagatgactcgctgggagaattctcactgaaaagttaaatgtggatgttttcccatccgggataatgcagACAAGGCATTATTCGGGGAGAGAGAGTGGTATTTCTTTTCGCCAAGGGACAGGAAGTACCCCAATGGCGCAAGGCCCAACAGAGCCGCCGCAAGCGGCTA
- - tgatgca