Sequence
atgc intronic sequence ATGC exonic sequencegtttttgcttttaaaatacggtcttctaagttattcccataaattttttggactttccctctaatctttgttgtttccttcaacagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05190.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G06690.1 (Glycine max), 3'ss of exon 16
----gtttttgcttttaaaatacggtcttctaagttat-tcccataaattttttggactttccctc----taatctttgttgtttccttcaacagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
| |||| ||| | | | | | || | | | || |||| | ||| | |||| || ||| | | |||||||| |||||||| | || | ||||| ||||| |||||||| ||||||||||||||||| ||||| ||||| || || |||||| | ||| | | |
gtatctatttgatttgcatttctgtgaatttgagctctctgtcaacaattctacttttttttaataacagtaattttctttgctgtcacattcagGCTATCAACAAAAGTCTCTCGTCTTTGAGCGATGTCATATTTGCTTTGGCAAAGAAAGAGGAGCATGTTCCTTTTAGGAATTCAAAGCTGACACACTTTC
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA13G32450.1 (Glycine max), 3'ss of exon 14
--------------gtttttgcttttaaaatacggtcttctaagttattcccataaattttttgg-actttccctctaat---ctttgttgtttccttcaa---cagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
|||| ||| || | || | ||| | |||| | | | |||| |||| | | | || | |||||||| |||||||| | || | ||||||||||| |||||||| |||||||||||| |||| |||||||| || || || ||||| || ||||| || |
gtgtctctttgattcattttattttattaacttgagctctatgtcggaaactttaagtcttttactaataaacaggtaatgaattttgctatgtttatctatgtcagGCTATCAACAAAAGTCTCTCCTCTTTGAGTGATGTCATATTTGCTTTGGCAAAGAAACAGGAGCATGTACCCTTTAGGAATTCAAAATTGACATACCTTC
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA07G30580.1 (Glycine max), 3'ss of exon 14
gtttttgcttttaaaatacggtcttctaagtta----ttcccataaattttttggactttccctc--------taatctttgttgtttccttcaacagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
|| | | ||||| | || | | | | || | | | || || | |||| | |||| | ||| | | |||||||| |||||||| | || | ||||| ||||| |||||||| ||||||||||||||||| ||||| ||||| || || |||||| | ||| | | |
gtatcta--tttaatttgcgttgctatgaatttgagctctctgtcaacaattctaattttcttttaataacagtaatttgctttgctgtcacattcagGCTATCAACAAAAGTCTCTCATCCTTGAGCGATGTCATATTTGCTTTGGCAAAGAAAGAGGAGCATGTTCCTTTTAGGAATTCAAAGCTGACACACTTTC
upper sequence: AT4G05190.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA15G06880.1 (Glycine max), 3'ss of exon 15
gtttttgcttttaaaatacggtcttctaagttattcccataaattttttggactttccctctaatctttgttgttt---ccttcaacagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
|| | || || | | | || | ||||| | | || | | | ||| |||| | | | ||| |||||||| |||||||| | || | ||||||||||| |||||||| |||||||||||| | || |||||||| || || || ||||| || ||||| || |
gtgtctgttt----ggttcattttttt---ttattaactttaactaat--aaacaggtaataaatttttgctatgtacatctttgtcagGCTATCAACAAAAGTCTCTCCTCTTTGAGTGATGTCATATTTGCTTTGGCAAAGAAACAAGAGCATGTACCCTTTAGGAATTCAAAATTGACATACCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcccataaattttttggactttccctctaatctttgttgtttccttcaacagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
ctctaat putative branch site (score: 3)
ctttccctctaatctt CT-rich tract
ataaattttttgga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgcttttaaaatacggtcttctaagttattcccataaattttttggactttccctctaatctttgttgtttccttcaacagGCTATAAACAAAAGCTTGTCTGCATTGAGTGATGTTATATTTGCATTGGCAAAGAAAGAGGATCATGTACCTTTCAGAAACTCAAAGTTAACATATCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT