Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G26800.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaac-caccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
| |||| || ||| || || | | ||| | || | | || | | || ||| | || | | ||| || || | | | | |||| |||||||||||| || |||||||| ||| | || || ||||| |||||||| |||| |||||||||||||||||| | |
-------------------------------------------------------------------gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 3
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccac-tacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
||| | || | ||| || | || || | | || ||||| | || | | | ||| | | || ||| || || || | | | | |||| |||||||||||| || |||||||| ||| | || || ||||| |||||||| |||| |||||||||||||||||| | |
----------------------------------------------------------------------------------ataactaaata-agtgaaa-atggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaatt--gatgattaactggtt----ttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g16350.1 (Oryza sativa), 3'ss of exon 2
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccacc--atttttttttctctcttattctgttttttttctgtttggaattt--agATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
| ||| | | | | | | | | || || ||| | | | | || ||| | || | ||| | | | || |||| ||| | | | || | | ||| |||| | | | |||| |||||| ||||| |||||||| ||| ||||||| || ||||||||||| || ||||| || ||| ||||||| | |
-------------------------------------------------gtgggcagccatatgttaatgagcttctatgacagagcttgatatgttcagcctttagctttattaaaggaaaattgctgccatttttgttatagaagaattatttccttctgaatttattgactggaggcaacatgtttccagATTATACATGACCTTCCAAGAAGTGTGAAAATTGTGGAAGTTGGGCCACGAGATGGGCTACAGAATGAGAAGAACATAGTTCCAACACATGTAAAGATTG
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG-----------
||| ||| |||| | | | || |||| |||| | | |||||| | | | | ||||| | ||| | | | | || || || || |||||||||||||||| ||||| ||||||||||||||||| ||||| | || |||||||| || || ||||| || |||||||| | |
-----------------------------------------------------------------------------gtaatata-ttttaaactttttgttgtcgtttt-attt---tatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatg------atgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 4
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctctta--ttctgttttttttctgtttgg-aatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG----------
| ||| ||| ||| || || | | ||| || || ||| || | |||||||||||||| ||||| ||||| || |||||||||||||| ||||| | || ||||||||||| || ||||| ||| ||||||| | |
------------------------------------------------------------------------------------------------------------------------------------------gtatcatatttctttggctggtaagtaacatacaattttaattgggcaatgcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G04110.1 (Glycine max), 3'ss of exon 3
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtt-taaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
| | | | | || | || || ||| | || | | ||||| | | | | | ||||| | || | || || | || || | || |||||||||||||||| ||||| ||||||||||||||||| ||||| | || |||||||| || || || || |||||||| ||| | |
--------------------------------------------------------------------------------------atatattttaaactttctattgtttgtttattttatcacatttctttgtctagtaattagcatgttttcaatttt----taattggacaatggctatgatgcagTTTCTGAATAGTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTGCCTACATCTGTGAAGATTG
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G36340.1 (Glycine max), 3'ss of exon 2
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctctta--ttctgttttttttctgtttgg--aatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
| ||| || || | ||||| | || | | | ||| ||| || ||| || | | ||| | |||| ||| || | |||||||||||||| ||||| ||||| || |||||||||||||| ||||| | || ||||||||||| || ||||| ||| ||||||| | |
---------------------------------------------------------------------------------------------ttgacatttatgttatacatttatactttctgtagttggttgattttatcatatttcgttgtctggtaagtaacatacaatttttaattgggcaatgcagTTTATGAAAGGTATACCAAAATTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTG
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
|| || ||| ||||| || || | | || | | | | | | | || | ||| |||| | | | || | ||||| | || | | || | | |||||||||||||||||||||||| || |||||||||||||| ||||| |||| |||||||| ||||| ||||| ||| ||||||| ||||
--------------------------------------------------------------------------ta-ataatataattttgcat-----tttacaatctttgtgt-tactggagttgtttcat--------ctgatttattttattttatgttttatttttgtactttgataagagcagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG
upper sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S130_226V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgat-tcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaattt---agATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
| || ||||| | | || | | | | || |||| || | ||| | || |||| | || || | | | | || | |||| || || || | || | ||| || | || || | || | | ||||||||||||||||| || ||| |||||||| ||||||||||||| | | | ||||| || || |||||||
-------------------------------------------gtaaatgtccaccaaa---ttgtgctgagatttccctgagtaatttttgatgacgataccgtcgaactcatgac-attcgaagctgcgc-tcgctgaaactgtattttattggtgctagttgctgacgacgatgatatgcatttttacagCTACTGAAGGGGTTGCCCAGCTACGTGAAGATTGTAGAAGTAGGGCCACGAGATGGCTTGCAGAATGAGAAGACGACTATCCCCACCTCCGTTAAGGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
ccatttttttttctct CT-rich tract
ttattctgtttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG