Sequence
atgc intronic sequence ATGC exonic sequencegtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G07160.1 |
intron # | 39 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 39
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 5
------gtccgtactttttaactctttacaattaaaataataaaaatatatatatgc---------attaattctgtt-----------------tacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
||| || || || | || | | | | ||| || | | ||| | || ||||| | |||| |||||||| | |||||||| || ||||| || || || |||||||| || ||||||||||| ||||||||||| |||||||| ||||| |||| |
ctttggatccctatttggcaattgctttccactgcactaactcaaccgtggttgtgctgctgtcttgtgaacactgttgatattaaacgttattctgtagGTTGGCAAAGGTAGGGATGTTGGACTTAATCAGATTGCACTATTTGAAGGAAAAGTTGCTGGTGGAAATGGTGAACAAGTTCTTAGCCGAGACATATATA
upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 39
lower sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 42
gtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
|| || || | || || | |||| | | | || ||| ||||||||| || || || ||||||||||||||||||| || || || |||||||| || ||| ||||||| || |||||||| ||||| ||||| ||||||||||
----gtgagacttgttgtttaatgatgcctctacaacaaatccttttcta-at--attaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 39
lower sequence: GLYMA10G44150.1 (Glycine max), 3'ss of exon 40
gtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
|| | |||| || | || | | | || ||| | | || ||||| ||||||||| || || || ||||||||||||||||||| || || || |||||||| || ||| ||||||| || |||||||| ||||| || || ||||||||||
gtgag-acttgttgtttattgatccctcta-caacaaatcgttttcta-atattaa----atttacagGTTGGTAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGCCGTGATGTATACA
upper sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 39
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
-----gtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
| || || | | | || ||||| | || ||||| | || | | ||| |||||||||| || ||||| ||||||||||| |||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| ||||| |||||||| | ||||
gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaa-atctctaatctaa----gtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
ttctgttt CT-rich tract
tttacaattaaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG