Sequence
atgc intronic sequence ATGC exonic sequence...cagaaagttttcttgattgccaatcagtttactatttttatacattgaatttaaaaaaactaatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
Basic information
species | Physcomitrella patens |
transcript | PP1S149_164V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G017520_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------cagaaagttttcttgattgccaatcagtttactatttttatacattgaatttaaaaaaactaatgtctatttcgtcgatca--cacacaattgctg-taacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
| |||| || | || |||| ||| || | || || | || | ||| | | |||| || | |||| ||||| ||||||| ||||||||||| ||| ||||||||||||| || | || || | ||| |||| | || || | || || || | | ||
gtacaaccatcaaaatcaaaatcaaatcctgcacgctttgctctaccttctcaattgtccatctccactgtttcctgctccttctccaaggctacttctttctcccaactcctcctctcgtacc--tgctcaattgattgattaattaattaattaatggtggcagGGCTTCAGAGGTGTGGCAAGAGCTGCAGGCTGAGGTGGATAAATTACCTGAGGCCTGACCTTAAAAGAGGCGCATTCTCTGAGGAGGAGGAAGACCTCAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G086746_T01 (Zea mays), 3'ss of exon 1
-----------------------cagaaagttttcttgattg--ccaat----cagtttactatttttatacattga-atttaaaaaaactaatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
| | | |||| ||| || | | ||| ||||| | | || | || | || | | | | || || | | |||| ||||| ||||||| ||||||||||| ||| ||||||||||||| || | || || | ||| |||| | ||| || || |||| | | ||
gtacaaccaaatccggcacactctattatatcttctcaatttatccgtttccactgttccctattcctctccaagaccacttctttcttcccattcttctcataccctgctcaattaacgatggcagcagGGCTTCAGAGGTGTGGCAAGAGCTGCAGGCTGAGGTGGATAAATTACCTGAGGCCTGACCTTAAAAGAGGCGCGTTCTCTCAGGAGTAAGACCTTATAAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA03G38660.1 (Glycine max), 3'ss of exon 1
------------------cagaaagttttcttgattgccaatcagtttactatttttatacattg-aatttaaaaaaactaatgtctattt---cgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
| || ||| | || | | | | ||| | ||| || |||| | | || || | || || | || | || ||| |||||||||| ||||||| |||||||||||| | ||||||||||||||||| | || |||||||| |||||| || ||| | ||||||||||| ||
gtaggatgatgagtactatacaacactttatcaatattaatattgcatcatgtttgtccacaacacaacacaaaagtcattttacttaattaaccttccttctctcaaactttgtgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGGTGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAAGAAGAGAATTCCAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G41250.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------------------------cagaaagttttcttgattgccaatcagtttactatttttatacattgaatttaaaaaaact-aatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
||| | || | | | | ||| | |||| || ||| | || | || | || || | | | | | ||| |||||||||| ||||||| |||||||||||| | | ||||||||||||||| | || |||||||| |||||| || ||| | |||||||| | ||
gtaggatgatgagtactatactatacaatacttcatgtttccatcatcactttatcaatatattgttgctgcagcatgtgcacaacacaacacaaaagtc-atcatttgaattaattaaccttccttttttttaagatttaatttttttgtgttgtatatct--tgtctcagGTCTTCAGAGGTGTGGCAAGAGCTGCAGATTAAGATGGATAAATTATCTCAGGCCTGATTTGAAGAGAGGAGCATTCTCACAGCAGGAAGAGAACTCCAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------cagaaagttttcttgattgccaatcagtttacta---tttttatacattgaatttaaaaaaactaatgtctatttcgtcgatcaca----cacaattgc------tgtaac-agGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
| ||| || || | ||| | | || || | | | | |||| | | ||| | || | | || |||| | ||| ||| ||||| ||||||||||||| |||||| | | |||||||||||||| |||| ||||||||||| ||| || || | ||||| | ||
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctgagtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 1
--------------------------------------cagaaagttttcttgattgccaat------cagtttactatttttatacatt--------gaatttaaaaaaactaatgtct-atttcgtcgatcacaca--caattgctgta------acagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
|| | ||||||| ||| || | | | | | || | ||| | ||| || || | | | | | || | | |||| | | |||| || || ||||||||||||| |||||| | | |||||||||||||| |||| ||||||||||| ||| || | | ||||| | ||
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G01050.1 (Glycine max), 3'ss of exon 1
---------------------------------------cagaaagttttcttgattgccaatcagtttactatttttatacattgaat-----ttaaaaaaactaatgtctatttcgtcgatcacacacaat-tgctgtaa---cagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
|| |||| || | || | |||| | ||| || |||| | | |||||| | | ||| || | || || ||| ||| ||||| ||||||||||||| |||||| | | |||||||||||||| |||| ||||||||||| ||| || || | | ||||| | ||
gtatatatatacatatataattaacaagtctaccctactattaatatttttttcagcacccttttgtttctcagttt-attcattaagtaggtcttaaaactttgagtttcttattaattatgtgttcatttcatgatgtgtgcctagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTGAAGAAGCAGCCCTCAT
upper sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
cagaaagttttcttgattgccaatcagtttactatttttatac-attgaatttaaaaaaactaatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
| ||| | | ||||| ||| | | | | | |||| | | | | | ||| | | | | || ||||||| || | ||||||||||||||||||||| | ||||||||||| || |||| || || ||||| || || || | ||||| | | ||
-ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaatttaaaaaaactaatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
aactaat putative branch site (score: 2)
ttaaaaaaactaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagaaagttttcttgattgccaatcagtttactatttttatacattgaatttaaaaaaactaatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA