Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcaactgattcaggccctggaattgtgatgttcttgaaagcacgtgcttttgaatttcatcacttggaccagaatctggatattattaagtgatgaatacttcgtcgattttagGTTTGTGGAAAATGGATCTCTGGCTAGCATAATTAAACCAAACAAATTTGGAGCGTTTCCAGAATCTTTGGTCGCTGTGTACATTGCCCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S99_12V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 4
gtaagttcaactgattcaggccctggaattgtgatgttcttgaaagcacgtgcttttgaatttcatcacttggaccagaatctggatattattaagtgatgaatacttcgtcgattttagGTTTGTGGAAAATGGATCTCTGGCTAGCATAATTAAACCAAACAAATTTGGAGCGTTTCCAGAATCTTTGGTCGCTGTGTACATTGCCCAG
||||| ||| | | || | | | || | | || | | |||| || | | || | || | | || | ||| |||| |||||| ||||| || || |||| || || || ||||||||||| ||| | ||||| ||||||||||| ||||| |||||||| |||
gtaag--caattatcgttgaaaatgtcttcatagttgatacgaga-tagatgtatacagtatacatctagtgaatttcgacatgtaagttctaataccatagggat------aattgcagGTATGTGGAGAATGGCTCACTTGCTAATATTATCAAGCCAAACAAATTCGGACCTTTTCCTGAATCTTTGGTGGCTGTATACATTGCTCAG
upper sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttcaactgattcaggccctggaattgtgatgttcttgaaagcacgtgcttttgaatttcatcacttggaccagaatctggatattattaagtgatgaatacttcgtcgattttagGTTTGTGGAAAATGGATCTCTGGCTAGCATAATTAAACCAAACAAATTTGGAGCGTTTCCAGAATCTTTGGTCGCTGTGTACATTGCCCAG
| | | | | || ||| |||| | | | | |||| ||| || ||||| |||||||||||||| |||| || ||||||||||| || |||||||| || | || ||
---------------------------------------------------------------------gtaagcta-accgtcaatgttagcct-tgattagtgtggttttctctgcagGTATGTCGAGAATGGTTCTCTGGCTAGCATTGTTAAGCCGAACAAATTTGGCGCATTTCCAGAGTCACTTGTTGCC---------------
upper sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ14289 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttcaactgattcaggccctggaattgtgatgttcttgaaagcacgtgcttttgaatttcatcacttggaccagaatctggatattattaagtgatgaatacttcgtcgattttagGTTTGTGGAAAATGGATCTCTGGCTAGCATAATTAAACCAAACAAATTTGGAGCGTTTCCAGAATCTTTGGTCGCTGTGTACATTGCCCAG---------
| | | | ||| | | || | |||| | | || | |||| ||| || ||||| |||||||||||||| |||| || ||||||||||| || |||||||| || | || ||||| |||||||| |||
----------------------------------------------------------------gtaagctaaccgtcaatgttggccttgattagtgtggttttctctgc-------agGTATGTCGAGAATGGTTCTCTGGCTAGCATTGTTAAGCCGAACAAATTTGGCGCATTTCCAGAGTCACTTGTTGCTGTATACATTGCTCAGGCATGTATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacttggaccagaatctggatattattaagtgatgaatacttcgtcgattttagGTTTGTGGAAAATGGATCTCTGGCTAGCATAATTAAACCAAACAAATTTGGAGCGTTTCCAGAATCTTTGGTCGCTGTGTACATTGCCCAG
cttcgtc CT-rich tract
atattattaagtgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcaactgattcaggccctggaattgtgatgttcttgaaagcacgtgcttttgaatttcatcacttggaccagaatctggatattattaagtgatgaatacttcgtcgattttagGTTTGTGGAAAATGGATCTCTGGCTAGCATAATTAAACCAAACAAATTTGGAGCGTTTCCAGAATCTTTGGTCGCTGTGTACATTGCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG