Sequence
atgc intronic sequence ATGC exonic sequence...gttgcttttgagccgagtagtccagtctactctcaatatgttgggaattttttctatttttctgactccatgtttactgttgttgcaatgatttttgcagTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA
Basic information
species | Physcomitrella patens |
transcript | PP1S302_9V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S302_9V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------gttgcttttgagccgagtagtccagt--ctactctcaatatgttgggaattttttctatttttctgac-------------tccatgtttactgttgttgc--aatgat-ttttgcagTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA
||| ||| || || | ||| | ||| | || | || | || | | | | || | || | || || | || | ||||||| ||||| || ||||| || || ||||| |||||||| ||||| ||||||||||| ||||| || || || || || | ||||| | || || | ||
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
upper sequence: PP1S302_9V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G38340.1 (Arabidopsis thaliana), 3'ss of exon 3
gttgcttttgagccgagtagtccagtctactctcaatatgttgggaattttttctatttttctgactccatgtttactgttgttgcaatgatttttgcagTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA
|| ||| | | || || | | ||| || || ||| | | | | ||| | | ||||||||||||| || || | ||||| ||||| |||||| ||||||||||||||||||| || | || ||||| |||||| | | || | |||| ||||
----------------gtgcgtcagagtttttataaaatttgaattgatatttacatattatgatgatgatgatgatcatgatggcattacatattgcagTATGTCCGACGACCTTGAAGAGGATATGCAGACAAAACGGAATCTCAAGGTGGCCATCGAGGAAGATCAAGAAAGTTGGACATTCTCTTCGAAAACTGCA
upper sequence: PP1S302_9V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G64530.1 (Arabidopsis thaliana), 3'ss of exon 4
gttgcttttgagccgagtagtccagtctactctcaatatgttgggaattttttctatttttctgactccatgtttactgttgttgcaatgatttttgc-agTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA
|| | ||| || || | | | || || || | | | | || | ||| | ||||| | ||| || |||||||| | || | || || |||||||||| |||||| ||||||| |||||||||||||| || || | ||||| | | | | | |
------------------------gtatgttcttaactc--tgtgtactaattgtaattgttgataacaaactctaaaaattttgtgctacttttttccagTTTGCCCAACAACAATGAAACGCATTTGCCGACAACACGGGATCTCACGGTGGCCATCTCGAAAAATCAACAAGGTGAACCGATCTCTCACACGACTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttttctatttttctgactccatgtttactgttgttgcaatgatttttgcagTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA
ttctgac putative branch site (score: 2)
tttttgc putative PPT
tttctattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcttttgagccgagtagtccagtctactctcaatatgttgggaattttttctatttttctgactccatgtttactgttgttgcaatgatttttgcagTATGTCCAACAACGCTCAAGAGAATATGTAGACAACACGGAATCTCAAGGTGGCCTTCTCGAAAAATCAATAAAGTTAGTCGATCGTTGAAAAAATTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca