Sequence
atgc intronic sequence ATGC exonic sequencegtaattatcatttgtttgatagtttgtagtactgtttttaatgttttggagtatgatgttatatttaacatgatttggttgctaatatagGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G19230.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G19230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G20490.1 (Glycine max), 3'ss of exon 5
----------------------gtaattatca-tttgtttgatagtttgtag----tactgtttttaatgttttggagta----tgatgttatatt--taacatgatttggttgctaatat----agGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
| ||| | | ||| || || ||| || |||| || || | || ||| | | | | ||||| | || | |||| | |||| |||| |||||||||||| || ||||||||||||||||| ||||| | |||||||| ||||||||||| ||| | ||||| | | | | ||||
gtaattatttagcagaagttatgcaatccttactttcctttattttttatatactttactattcatatcatacctacgtgtttctgagctcagactcttaacagattctgttaaataattttgctagGTTGCTCTAAAACCCAATACTTTTATGCCATTTGGCAATGGGACCCATGCATGTCCTGGCAATGAATTAGCTAAGTTGGAGATTTTGGTGTTTCTACATC
upper sequence: AT4G19230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G08340.1 (Glycine max), 3'ss of exon 5
-------------------------------------gtaattatcatttgtttgata-gtttgtagtactgttttta-atgttttggagtatgatgttatatttaacatgatttggttgcta---atatagGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
| | || ||| ||| | | | | || || || ||||| || || || | || || || ||||| ||||||||||||||||| || ||||||||||||||||| || | | |||||||| |||||||||||||| | ||||| | | | | ||||
gtatttattgtgcagaacatatgcaatccttattttttttttaattttttatttactttgctattcatatcattcctacgtgtttctaagctcagacttctaacagattctgttaaattattatgctagtagGTTGCTCCAAAACCCAATACTTTTATGCCATTTGGCAATGGGACACGTGCATGTCCTGGCAATGAATTAGCCAACTTGGAGATTTTGGTGTTTTTACATC
upper sequence: AT4G19230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G14310.1 (Glycine max), 3'ss of exon 5
----------------------------gtaattatcatttg-tttgatagtttgta-gtactgttttta-atgttttggagtatgatgttatatttaacatgatttggttgctaatatagGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
||| || | ||| ||| | | | | || | || ||| || || | || || || | ||| || | ||||| ||||||||||||||||| || |||||||||||| |||| |||| | |||||||| |||||||||||| || | ||||| | | | | ||||
gtgcataacatatgcatttcctactttcgtattttttttttaatttacttttctatccatatcatacctacatgattctaagcccaaactt-taacaaattttattaaattattttgctagGTTGCTCCAAAACCCAATACCTTTATGCCATTTGGCGATGGGGCCCATGCATGTCCTGGCAATGAATTAGCCCAGTTGGAGATTTTGGTGCTTCTACATC
upper sequence: AT4G19230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G35660.2 (Glycine max), 3'ss of exon 4
--------------gtaattatcatttgtttgatagtttgtagtactgtttttaatgttttggagtatgatgttata---tttaacatgatttggttgctaatat---agGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
| || || ||| | | | ||| |||| || | | || || | || | || ||| | || || | || | ||| |||||||| ||||| || || ||||||||||||| ||| | |||| |||||| || ||||||||||||||| | ||||| | | | | ||||
gtaattattgtgctgaaaccatgttttacctaccaacct-cagttttgttgctattcatgtgtgataccaagtccaagaccttgacagattctgtttaattatttgccagGCTGCTCCAAAGCCCAACACTTTTATGCCATTTGGCAGTGGGATCCACATGTGTCCAGGGAATGAATTAGCCAAGTTGGAGATTTTGGTCCTCCTACATC
upper sequence: AT4G19230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G35250.1 (Glycine max), 3'ss of exon 5
----gtaattatcat-ttgtttg----------atagtttgtagtactgttt-ttaatgt----tttggagt-----atgatgttatatttaaca---tgatttggttgctaatat---agGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
|||||||| | ||||| | ||||| | | || || || |||| | ||| | || || | || | | | | || || | || | ||| |||||||||||||| || || ||||||||||||| ||| | |||| |||||| || || |||||||||||| | ||||| | | | | ||||
gtaagtaattattgtgctgtttacctaccaagcacagttt-tgttgctattcattcatgtgtgatcccaagtcagtcaagaccttgaaattgagagattcttctgtttaattatttgccagGCTGCTCCAAAACCCAACACTTTTATGCCATTTGGCAGTGGGATCCACATGTGTCCAGGGAACGAATTAGCCAAGTTGGAGATTTTGGTCCTCCTACATC
upper sequence: AT4G19230.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0087g00710.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtaatt--atcatttgtttgatagt-ttgtagtactgtttttaatgttttggagtatgatgttatatttaacatgatttgg-ttgctaat---atagGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
| ||| || || | | | ||| || || || || |||| | | | | ||| | | || || || || | |||| | |||| |||||||| |||||||| || ||||||||||| ||||| |||||| || ||||| ||||| || ||||| || ||||| | | | | ||||
gtaaaaagagaaaacaaaatgattgaatgatattgtgggtagcgttttaataatggttttccagcacccaa-tctaatgatgtgaacaatatttttgggatcaataattggacagGTTGCTCCAAAGCCCAATACATTTATGCCATTTGGAAATGGGGTCCACTCATGCCCTGGGAATGAGTTGGCCAAACTAGAGATTTTGGTGCTTCTACATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaatgttttggagtatgatgttatatttaacatgatttggttgctaatatagGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
tgctaat putative branch site (score: 2)
atgttatatttaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattatcatttgtttgatagtttgtagtactgtttttaatgttttggagtatgatgttatatttaacatgatttggttgctaatatagGTGGCTCCAAAACCCAATACGTTCATGCCATTTGGCAATGGAACCCACTCGTGTCCTGGAAATGAATTAGCCAAGCTTGAGATGTCTATTATGATTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG