Sequence
atgc intronic sequence ATGC exonic sequence...tgtcaatcaggttcatgtacttgacgcgcataaaggtttaatgaccagatttgaggtggtcgatgcgtaatgttttgatactacctgttgccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S47_46V6.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 4
------------tgtcaatcaggttcatgtacttgacgcgcataa--aggtttaatgaccagatttgaggtggtcgatgcgtaatgttttga----tactacctgttgccatccaca-----gGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
| ||| | || | | |||| || | || || ||| || | | || | | ||| ||| | |||| | | | || ||| ||| || | || || || ||||| ||||| || || || |||| |||| ||||| ||||||||||||||||||||| |||||
gtaagttcaagaaataaatttgcttaggaatacaaaatcacatagttagctcaaagcctcaaattaatggctgcccattttaatgatcttggggtgtaccaaatgttactttactcattcaagGGCGTGCTGCTCTACGGTCCACCTGGAACTGGGAAGACGCTCCTAGCTAGAGCCATTGCTAGCAACATTGATGCTAATTTTTTGAAG
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------tgtcaatcaggttcatgtacttgacgcgcataaaggtttaatgaccagatttgaggtg-gtcgatgcgtaatgttttgatactacct--gttgccatc-cacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
||||| | || | || | | || | | || ||| | | | ||| | || || || || | |||||||| | | |||||||||||||| ||||| ||||| | ||||| | ||||||||||| ||||| |||||||| || ||||
ggtgattacttttcactgtactacttggtctttggcctctattgtatgtgttttggcagcattgtcacctaagtatccacattttcttttggtggaagtgtgttttgaggagccatggtttatagttttgtatctgatcaatttcttctcaattcttgtctcccaGGGTGTTCTTCTTTATGGGCCTCCTGGTACTGGGAAAACATTGTTAGCTAGGGCAATTGCCAGTAACATAGATGCTAACTTCTTGAA-
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------tgtcaatcaggttcatgtacttgacgcgcataaaggtttaatgaccagatttgaggtg-gtcgatgcgtaatgttttgatactacct--gttgccatc-cacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
||||| | || | || | | || | | | || ||| | | | ||| | ||| || || || | |||||||| | | |||||||||||||| ||||||||||| | ||||| | ||||||||||| ||||| || ||||| || |||||
gtgattacttttcactgtactacttggtctttggcctctattgtatttgttttggcagcattgtcacctaagtatccacaatttcttttggtggatgtgtgtttagaggagccatggtttatagttttgtatctgatcgatttcttctcaattcttgtctcccagGGTGTTCTCCTTTATGGGCCTCCTGGTACTGGTAAAACATTGTTAGCTAGGGCAATTGCCAGTAACATAGAAGCTAACTTCTTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagatttgaggtggtcgatgcgtaatgttttgatactacctgttgccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
ttttgat putative branch site (score: 4)
taatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcaatcaggttcatgtacttgacgcgcataaaggtttaatgaccagatttgaggtggtcgatgcgtaatgttttgatactacctgttgccatccacagGGTGTGTTGTTATATGGGCCTCCTGGGACTGGTAAAACTCTTTTAGCACGAGCAATTGCCAGCAACATTGATGCTAATTTTCTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG