Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttatcggtttctgaatgtatcgatgagatgcttcggcttctaatgatacttggattaaatgttttttagttttcttgtagagaagATGGGAGTGTCTTCTGCGTCAAGGAAGGAGGGTATTTGTTGTTGGGGATCTCAACATTGCTCCTTTTGCTATGGATCGATGTGAAGCTGGGCCTGATTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G05430.1 (Glycine max), 3'ss of exon 4
----------gtaagttta-tcggtttctgaatgtatcgatgagatgcttcggcttctaatgatacttggattaaatgttttt--tagttttcttg-tagagaagATGGGAGTGTCTTCTGCGTCAAGGAAGGAGGGTATTTGTTGTTGGGGATCTCAACATTGCTCCTTTTGCTATGGATCGATGTGAAGCTGGGCCTGATTTT
| |||| || |||| | || | ||| | ||| || | | | | || | || | || |||| | || |||| ||||||||||| ||| |||| |||||||||||| ||||||||||||| |||||||| ||||| || ||||| || ||||||||||| || || ||||
cagtgctcatttttttttactctgttttcttgtatagagctgaaaattttcttttttcttttgttttctgtttgattgatgttgatagtctctttaatagAAAAGATGGGAGTCTCTCCTGCATCAAGGAAGGAGAATATTTGTTGTTGGTGATCTCAATATTGCACCATTTGCAATTGATCGATGTGATGCCGGACCTG-----
upper sequence: AT4G36050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G23850.1 (Glycine max), 3'ss of exon 5
---------gtaagtttatcggtttctgaatgtatcga--tgagatgcttcggcttctaatgatacttggattaaatgttttt--tagttttcttg-tagagaagATGGGAGTGTCTTCTGCGTCAAGGAAGGAGGGTATTTGTTGTTGGGGATCTCAACATTGCTCCTTTTGCTATGGATCGATGTGAAGCTGGGCCTGATTTT
| ||| || | | | ||||| || | | || |||| || | | | | || | || | || |||| | || |||| |||||||| || || ||| |||||||||||| |||||||||||| |||||||| ||||| || ||||| || ||||||||||| || ||||
gtgcagtgcttgtttttttctgactgtttttgtatagaactcaaatttttcgtttttcttttgttttctgtttgattgatgttgatagtctctttaatagAAAAGATGGGGGTCCCTCTTGCATCAAGGAAGGAGAATATTTGTTGTTGTTGATCTCAATATTGCGCCATTTGCAATTGATCGATGTGATATAGGACCTG-----
upper sequence: AT4G36050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g03440.t01 (Vitis vinifera), 3'ss of exon 4
------gta-agtttatcggtttctgaatgtatcgatgagatgctt-------cggcttctaatgatact-tggattaaatgttttttagttttcttgtagagaagATGGGAGTGTCTTCTGCGTCAAGGAAGGAGGGTATTTGTTGTTGGGGATCTCAACATTGCTCCTTTTGCTATGGATCGATGTGAAGCTGGGCCTGATTTT
|| | |||| | | | || | | ||| ||| ||| | | | ||||| || | || | | || ||| ||||||| |||||||||| ||| | || || || |||||| ||||||||||||| ||||| || ||||||||| |||||| ||||| ||||| ||||| || |
aagaaagtgcattttagctgcctttgta-gcatcacggagggtcttgttataataattcatcttcatactctgtgattgatatcggtaagctttgttgtagAAAAGATGGGAGACTCTCCAGCAGCAGGGGAGGAGGATATTTGTTGTTGGTGATCTTAATATTGCTCCTGCTGCTATAGATCGCTGTGATGCTGGACCAG----- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcggcttctaatgatacttggattaaatgttttttagttttcttgtagagaagATGGGAGTGTCTTCTGCGTCAAGGAAGGAGGGTATTTGTTGTTGGGGATCTCAACATTGCTCCTTTTGCTATGGATCGATGTGAAGCTGGGCCTGATTTT
ttctaat putative branch site (score: 2)
ttttttagttttctt putative PPT
attaaatgttttttag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttatcggtttctgaatgtatcgatgagatgcttcggcttctaatgatacttggattaaatgttttttagttttcttgtagagaagATGGGAGTGTCTTCTGCGTCAAGGAAGGAGGGTATTTGTTGTTGGGGATCTCAACATTGCTCCTTTTGCTATGGATCGATGTGAAGCTGGGCCTGATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG