Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctacttacgcttgaagtttatgaattgtgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattcatgaaatctagacgttaactgattctatgaggctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G33770.2 (Glycine max), 3'ss of exon 2
gtaagtctacttacgcttgaagtttatgaattgtgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattcatgaaatctagacgttaactgattctatgaggctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
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-------------------------------------------------gtatgtggtttgacgatgcgcaatgctgt--gaattcaatttatt-----ggccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAATCACAATCGAATGCACAAGCCATGTTCAATCTTGGATACATGCATGAGC
upper sequence: AT1G73570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G05930.1 (Glycine max), 3'ss of exon 2
gtaagtctacttacgcttgaagtttatgaattgtgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattcatgaaatctagacgttaactgattct-atgaggctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
||| | | || | | ||| | ||| || ||| | || | || || || | |||| || | | | || | | |||||||| | ||||||| | ||| || || ||||| || ||| |||||||||| |||| || |||||||| |||||||| || || |||||||||||||
----------------------------------------------------------------gtatgtggt----ttggcgatggatgaattcaatttaagccattgtgctctctttttgcctgcaccttttcactttctcgtgtttccctttttccttctgccagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAATCACAATTGAACGCGCAAGCCATGTTCAATCTTGGATACATGCATGAGC
upper sequence: AT1G73570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G05930.2 (Glycine max), 3'ss of exon 2
gtaagtctacttacgcttgaagtttatgaattg-tgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattcatgaaatctagacgttaactgattct-atgaggctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
| | | | || | || | | ||| |||| | | | | || | | ||| | ||| || ||| | || | || || || | |||| || | | | || | | |||||||| | ||||||| | ||| || || ||||| || ||| |||||||||| |||| || |||||||| |||||||| || || |||||||||||||
------------------gtaatgaacatgctgctttactcattggagatgcatattactatggtcgggtatgtggt-ttggcgatggatgaattcaatttaagccattgtgctctctttttgcctgcaccttttcactttctcgtgtttccctttttccttctgccagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAATCACAATTGAACGCGCAAGCCATGTTCAATCTTGGATACATGCATGAGC
upper sequence: AT1G73570.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv17s0000g02280.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtctacttacgcttgaagtttatgaattgtgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattca-tgaaa----tctagacgttaactgattctatgag-gctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
|| | | | || || |||| ||| ||| || | ||||| | | | || || ||| || || || ||| | || | | ||| || | || ||| |||||||| ||||| |||| | || || ||| |||| |||||| |||| || || ||||| ||||| ||||| ||||||||||| || |||||||||||||
--------------------------------gtatgtgtctataaatgggttaatcctgtcggagctctaggtccagg-acttctgattctagtatgcatttatgttctccatacaatgtaaattttcttaatttttatttatttattgtttaccttctttccctttctcagGGTACTGAGAGAGATTATGATCGAGCTGCAAAGGCATACATGCATGCCAAGTCCCAATCCAATGCACAAGCCATGTTCAACCTTGGGTACATGCATGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcatgaaatctagacgttaactgattctatgaggctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
aactgat putative branch site (score: 3)
aaatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctacttacgcttgaagtttatgaattgtgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattcatgaaatctagacgttaactgattctatgaggctcatactcatgttcacagGGTACAGAGAGGGATTTCGTGCGTGCAGCAGAGGCGTACATGTATGCTAAATCTCAATCAAATGCGCAAGCAATGTTCAACCTCGGTTACATGCATGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA