Sequence
atgc intronic sequence ATGC exonic sequencegtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
Basic information
| species | Arabidopsis thaliana |
| transcript | AT4G14360.2 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
-----------------gtgtctatcg----atatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaat-atgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
|| || || | ||||| | ||| || | | |||| | || | | || || | | | || ||||||| || |||||||||||||| | ||| |||||||||| || || || || ||||| ||||||||||||||||| ||||| || |||||| |||
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatcc--ttactac-acctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
--------gtgtctatcgatat---gttatacagttttatcgatatgatta-gttacgatga--cataactgttttctct----tccaatatgtttt-agGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
||| | || | |||| | | | | | | || ||| ||| | | ||| || | | |||| ||| |||| ||||||| || |||||||||||||| | |||| ||||||||||| ||||| || || ||||| |||||| | |||||||| ||||| |||||||||||||
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
---------gtgtct--atcgatatgttatacagtttta---tcgatatgattagttacg--atgacataactgttttctcttccaatatgtttt---agGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
||| | | || | || | | | | | | || || || | | | | |||| | | | | || | |||| |||| || || |||||||||||||| | |||| ||| ||||||| ||||| || || ||||| |||||| | |||||||| ||||| |||||||||||||
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
---------gtgtct--atcgatatgttatacagtttta---tcgatatgattagttacg--atgacataactgttttct-cttccaatatgtttt--agGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
||| | | || | | | | | | | | || || || | | | | |||| | | | |||| | |||| |||| || || |||||||||||||| | |||| ||| ||||||| ||||| || || ||||| |||||| | |||||||| ||||| |||||||||||||
taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttgattgcatccttgctgagctgtatccgacccacaattttttttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
----gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
| | | | ||| | || | |||| | | | ||| ||| |||| | | | | ||||| ||||||| ||||| |||||| ||||||||||||| |||||||||| || || || |||||||| |||||||| |||||||||||||| || |||||| ||
gtgaaaatttgctaagagtatatgtgatctt--caatatactctctgatactgatgtaattgttgtttat---ataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
------------------------gtgtctatcgatatgttatacagttttatcgatatgattagtta-------cgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
||| || | | | | | | || ||| || || | ||| | ||| || | ||| | ||||| || | || ||||| |||||| | ||||||||||| ||||||||||| || || || || ||||| |||||||| |||||||||||||| ||||||||| |||
gtaaagaatatgccgagactcgatgtgatcttcaactt-caacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
------------------------------gtgtctatcgatatgttat-acagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
| ||| | || | | | || ||| || | || | ||| ||| ||| | |||| |||| || ||||| |||||| | ||||||||||| |||||||||| || || || || || || ||||||||||||||||||||||| ||||||||| |||
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtc-taataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
---------------gtgtctat-cgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
| || ||| ||| | | ||| | | || || ||| | ||| || | ||| | ||||| |||| || ||||| |||||| ||||||||||||| || ||||||| || || || |||||||| |||||||| ||||| |||||||| || ||||||||||
gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgta-ttattttagtccaacatttgttgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 2
--------------------------------------gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataact-gttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
| ||| |||| | ||| || | || | || | | || | ||| | | | | || | |||||||| | || ||||| ||||||||||| | |||||||| | || ||||||||||| ||||||||| ||| || |||||||| |||||||||||||
gtgaaatttcactctccagggattgcttagtattagatggaactaa-gatagttcatagtgtatggaaaattttcttttgcttaagtatttagtttgttgtgttgttcttgataatatagGTTCCAGTCAAGTGGCCCAAAAGCAGAGACCAGGTGTGGAAGGCAAATATACCTCATACCCATCTTGCAACTGAAAAATCTGACCAGAACTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G34890.2 (Glycine max), 3'ss of exon 3
-----------------------------------------gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
| ||| || | | ||| || || | | || | | | |||| | | | | || |||||||| || || ||||| ||||||||||| | |||||||| | || ||||||||||| ||||| ||| ||| || |||||||| |||||||||||||
gtgacatttcattctccagagattgcttgatattattagatggaactaa-gacaattcatagtgtattgaaattttcttttgcttaagcatttaatttgttgtgttgttcttgataacatagGTTCCTATCAAGTGGCCCAAAAGCAGAGACCAGGTGTGGAAGGCAAATATACCTCATACCCATCTAGCAACTGAAAAATCTGACCAGAACTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
| || || | | || | | | | | | | | | || | | | || | || || | || || || ||||||||||||||||||||||| ||||||| ||||||||||||||||| |||||||||||||| |||||||| || ||||||||||
----gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
upper sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtgtctatcgatatgtt-------atacagttt-tatcgatatgattagttacgatgacataactgttttctcttccaatatg-----ttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
|| | | || || || | ||||| ||| | | | |||| || || ||| |||||||| | || | |||| || || || ||||| |||||||||||||| |||||||||| || ||||||||||| || |||||| ||||||||||||||| |||||||||||||
gtgagtctgtgcttaagttttttgaaatattgggaccaaggaagtttatattgttttcattatccacatgtacctaagatgattctcttctgctgtgggcggtaacagGTCCCAATCAAGTGGCCTAAAAGCAGAGATGAGGTGTGGAAAGCCAATATACCTCATACCCACCTTGCAACTGAGAAGTCTGACCAGAACTGGATGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
acataac putative branch site (score: 3)
ttttctcttccaat putative PPT
aatatgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
