Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcatacatatctctaactgctcttctttctccatttgcgatggttacataaaaaaaaaatcgattttgacatgtgacagGTATGAAGTACGACCTAAGAAGAGTGGAAGAAGTTTACTATGATGTCAAGATCCGAGGTTTGATTTCCGGCGGAGATCCTCCTGGCGTCCAAGCAGTCCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G37020.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G37020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G36680.1 (Glycine max), 3'ss of exon 6
---------------gtaagtcatacatatctctaactgctcttctttctccatttgcgatggttacataaaaaaaaaatcgattttgaca-tgtgacagGTATGAAGTACGACCTAAGAAGAGTGGAAGAAGTTTACTATGATGTCAAGATCCGAGGTTTGATTTCCGGCGGAGATCCTCCTGGCGTCCAAGCAGTCCA
|||| || | | | | | | | || | | | | | | | | || |||| |||||||| ||| |||||| ||| |||||||||||||||||||| ||||| || ||||||| | || || || ||| | | | || |
aaaaactatgtgtgcttaaggtatttgtgcagttggcatggagtttgtattcactcgtaccttctgtttggttgatatctttccactattggcttggcagGCATGAAGTATGACTTAAGAAAAGTCGAAGAAGTTTACTATGATGTTAAGATTCGGGGTTTGACACCGAATGGTGAGCCAGTTGGAGACTTGGAGATCAA
upper sequence: AT2G37020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0040g01630.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------gtaagtcatacatatctctaactgctcttctt-tctccatttgcgatggttacataaaaaa-----aaaatcgattttgacatgtgacagGTATGAAGTACGACCTAAGAAGAGTGGAAGAAGTTTACTATGATGTCAAGATCCGAGGTTTGATTT------CCGGCGGAGATCCTCCTGGCGTCCAAGCAGTCCA
| || | ||| | | | | ||| | | ||| | | | || ||| | | | | ||| |||| |||| |||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||| ||| | | | | || | | || | |
gtacagaatttactttgatcttattccacttttactaatattggaccaaatgtatattagattctttctctcattttcatgaacaaagttttcatctctgacttgcatgaaaaactttattttgtgccagGAATGAAGTATGACCTGAGAAGAGTTGAAGAAGTTTACTATGATGTTAAGATCCGAGGCTTGGCTGACAAAGCTGAAGAAGTTTCCTATGATATTAAGAT------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctccatttgcgatggttacataaaaaaaaaatcgattttgacatgtgacagGTATGAAGTACGACCTAAGAAGAGTGGAAGAAGTTTACTATGATGTCAAGATCCGAGGTTTGATTTCCGGCGGAGATCCTCCTGGCGTCCAAGCAGTCCA
ttttgac putative branch site (score: 3)
ttacataaaaaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcatacatatctctaactgctcttctttctccatttgcgatggttacataaaaaaaaaatcgattttgacatgtgacagGTATGAAGTACGACCTAAGAAGAGTGGAAGAAGTTTACTATGATGTCAAGATCCGAGGTTTGATTTCCGGCGGAGATCCTCCTGGCGTCCAAGCAGTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC