Sequence
atgc intronic sequence ATGC exonic sequencegtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S68_6V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G445617_T02 (Zea mays), 3'ss of exon 9
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
|| || || || ||| | || | | |||| |||| || | | | || | | | || || | | || | | || || || ||| || || || || |||| || ||||| || || || || ||||| ||| | ||||||||||| || ||||||||||| || || || |||||||| ||||||| |||||||| |
-------gtaggtttgaaaaggttc--catccggatt-caattgtattttt-----------gtttagctaccaataacaagtgcatc--cagaagaaacatgatacgag---atcgctaaaataatt--gtcccttggacttc------tagACTTTACTCGCGAAAGCAGTAGCAACTGAATGCTCATTGAACTTTCTTAGCGTCAAAGGTCCAGAACTGATAAACATGTATGTTGGAGAATCAGAGAAAA
upper sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA19G39580.1 (Glycine max), 3'ss of exon 9
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
| || | || | |||| | | || | |||| | | || | || || ||| | || | | || | | || | | | | ||| | |||||||| | || || |||||||| || |||||| | || || ||||| ||||| ||||||||||| || ||||||||||||||||||||||| || ||||
------------------------------gtaagttgtaatgtaactgtaaatgaca--atgttctacct----catttgtctaacgttttac-ttaaaaaaat---atttc-taac---accattttcttgctcttttattta-ataacagACATTATTAGCAAAAGCTGTTGCTACAGAGTGCTCCTTAAATTTTCTTAGTGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGA
upper sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA03G36930.1 (Glycine max), 3'ss of exon 14
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAG--GCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA-----------------------
| ||| ||| | | | || || | || ||| || | | ||| | ||| | | | || | | || || | | ||| | |||||||| | || || |||||||| || |||| | || || ||||| || || ||||||||||| || ||||||||||||||||||||||| || ||||
------------------------------gtgatctggtgttcttttgtacctg-taaatgacaatgctct--acctcatttctgttacttttatcttaaaaa----gatttaaaac---accattttctcactcttttatttaa--tacagacattattagcaaaaaagctgttgctacatagtgttccttaaattttcttagCGTGAAAGGTCCTGAACTGATCAACATGTACATTGGAGAGTCTGAAAAGAATGTTCGAGACATTTTCCAGAAG
upper sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G03000.1 (Arabidopsis thaliana), 3'ss of exon 8
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaaca-ctaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
| || ||| | | || | | || | | | | || || || | ||| || | | || || | || || ||||| || || || || ||||| || || |||||| | || || || || ||||| || ||||| || | ||||||||||| ||||||||||||||||| |
------------------------------------------------------gtaagtaagccatttttt---ctttc-----acttttagcatctcttaatagtctgttttttggcagttatatttttgagtttttgaattaaatttacagACTTTACTGGCAAAAGCTGTGGCGACAGAGTGCTCCTTAAATTTCCTCAGTGTAAAGGGTCCAGAATTAATCAACATGTATATTGGAGAGTCAGAGAAAA
upper sequence: PP1S68_6V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv07s0104g01610.t01 (Vitis vinifera), 3'ss of exon 9
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
||| || | | |||| || | ||| | | | | || | | || ||| || | ||| | | ||||| ||| || | | ||| | | || | | ||||| || | || || |||||||| || |||||| | | || ||||||||||| ||||| ||||| || ||||||||||| || ||||| |||||||| |
-------gtaagtttttgtttgttagccac-----ttatggtgatatctc-------aatacgttatttcttgtttatt-------tttttaac----caggaacctggtt-cattgctttcttggttac---tcctattgcaaatct--cagACTTTATTGGCAAAAGCTGTTGCAACAGAGTGCTCCCTCAATTTTCTGAGTGTAAAAGGGCCTGAACTGATCAACATGTATATAGGAGAATCAGAGAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
attatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataagataatttcgagctcattagacatgctgactgcggttgtgctttttatgatagaaagtcttgttctgaacattaggcaaattatcaacactaccaaagtttggttgcatgactgaatcgattatgtaccgtgatgtttgtgttgcagACATTGCTCGCCAAGGCTGTTGCCACTGAGTGCGCGTTGAACTTTCTGAGTGTCAAAGGTCCTGAGCTCATCAACATGTACATTGGAGAGTCAGAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA