Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G13370.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 6
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattatttta-atatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
||| | | | |||| || | | ||| | | | || || | |||| ||| | | || | || ||||| || |||||||| ||||| || |||||||| || |||||||| || || || |||||||||||||| || ||||| ||||| || || | | | |
---------------------------------------------------------caaagaaaatagcattaacaaa-acacagattcttctgcaggcacatttaaatgtctgg--ttatttaaattattctagctaacttgattattgcatatgcagGTCTCGCTTTTAAATATCGTTGTTGAGTTGAAAAAGTGCTGCAACCACCCATTTTTATTTGAAAGTGCTGATCATGGTTATGGTGGAGATAGCATTGGTG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 19
-----------------------gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagtt----acaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
||| | | | || | ||| | | | || || || || | || || | | || || ||| ||| | | | ||| | || ||| | | | | |||| || | | ||||| |||||| | ||||| || || || ||||||||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| || || | | || |
gtgagccaaatctgctctcccatgtgggcaaggattgattgtttataacttcatgtctgatctactaaattcaaataattagtgtgcttggtaacaattgttcttaaggcacatccaaatctgccctccaaaaaattagtgtcctgctatcatgttttatgtgactgacttgttaatgacatgcagGTATCACTTCTTAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTCTTGTTTGAAAGTGCCGATCATGGTTATGGTGGAGATAGCATCGGTG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 16
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
|| || | |||||| ||| | | | | | ||| | | | || | | | | ||| || | || ||||| |||||||| ||||| || || || ||||||||||||||||| ||||| || || ||||||||||| || || || ||||| || || | | |
----------------------------------------------------------gttcctcacctcactgtgcattacctagcaaactggagcatgggcacaaggcaacac-ttggccattggctaccaaactgacttgatcatggcatatgcagGTATCACTTTTGAACATTGTTGTTGAATTGAAGAAATGCTGCAACCATCCATTTTTGTTTGAAAGTGCCGATCACGGTTATGGTGGAGATAGCATTGGCG
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 17
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgt--aagttaggtgga---ttattt--taatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
||| |||| || || || | | ||| || |||| | || | | | | || | | | ||||| | | || |||||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||| ||||||||||| |||||||| ||||| || ||| | ||
------------------------------------------------------------------ctggactgacaaaattcggagaagttttaattcataatgtatatttctatattcttttctcttcaaagatcatcactaatctttttctgctaaatttcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 17
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaa---gctaac---aatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
| || | | |||| | |||||| | ||| || || || || || | |||| || | ||||| | | || | |||||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||| ||||||||||| |||||||| ||||| || ||| | ||
----------------------------------------------------------------actgacaaaatta-ttagaagttttatttcataatgtatatttatttctatattattttctcttaaaagattatctctaatctttttctgctaaatatcagGTTTCTCTTTTAAATATTGTGGTGGAATTAAAGAAGTGCTGCAACCATCCCTTCTTGTTTGAAAGTGCTGACCATGGCTATGGTGGGGACTCAGGAAGTA
upper sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 17
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
||||| || ||||||| | || ||| | || || | || ||| |||| | | | |||| || || ||||| | | | ||| |||||||||||| |||| || || || || |||||||||||||||||||||||||| |||||||||| ||||||||||| ||||| || ||| || |
--------------------------------gatttaactttctgaataact-cttgatttactcatg-gctattctttccccattccattgtaat---------------tgaact--ttgacata----tatcaatcctt---tcaaaattg-cagGTTTCACTTCTAAATATTGTTGTAGAATTGAAGAAATGCTGCAATCATCCTTTTCTATTTGAAAGCGCAGACCATGGTTATGGTGGGAACAGAAGTACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
agctaac putative branch site (score: 2)
tttgttgatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgactttatgatgcacccaggttctcatatttattgttatgaataattattttctttgtccctgcactgtaagttaggtggattattttaatatgcatccgacttcttaagtttgttgatattaagctaacaatctctgagttacaatcaacagGTTTCACTTTTAAACATCGTGGTGGAGTTGAAGAAATGCTGCAATCATCCTTTCTTATTTGAAAGTGCAGACCATGGATATGGGGGTGACATAAACGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA