Sequence
atgc intronic sequence ATGC exonic sequencegtaaggggtttcgtttggagctttggtgtctatcaggaactgagagatctcaatattttttgtccctgagttgcctttgattcattacagGTACAAAGGATTTCATGAGTATGCAAAGTCAAAAGGTGTGAATCTTGGTTCACCAGTTGGACTTGATGTGCTTGTTGATGGAATTGTTCCTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 3
------gtaaggggtttcgtttggagctttggtgtctatcaggaactgagagatctcaatattttttgtccctg----agttgcctttg-attcattacagGTACAAAGGATTTCATGAGTATGCAAAGTCAAAAGGTGTGAATCTTGGTTCACCAGTTGGACTTGATGTGCTTGTTGATGGAATTGTTCCTACAG
| || || | || ||| | || | || || | | || || | || || | | | ||| ||| | | ||||||||||| || ||||| |||||||||| ||||| |||||| ||||| ||| ||||||||||| || ||||||||||||| || || ||||
cttatggatagatgtggtgatttccttttttgggtgaacaagaaagagtgt-ataccattgttgttcaattcagtattaattgatattgtaactgctgtagGTACAAAGGTTTCCATGACTATGCAAAGTTGAAAGGAGTGAATGTTGGTGAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 3
-------gtaaggggtttcgtttggagctttgg-tgtctatcaggaactgagagatctcaatattt--tttgtccctgagttgcctttgattcattacagGTACAAAGGATTTCATGAGTATGCAAAGTCAAAAGGTGTGAATCTTGGTTCACCAGTTGGACTTGATGTGCTTGTTGATGGAATTGTTCCTACAG
|| | | |||| ||||| || | | | || | | || || | | | | | | ||||||||||| || ||||| |||||||| | ||||| ||| || |||| ||| ||||||||||| || ||||||||||||| || || ||||
cttagagatagatgtggtggtttccttttttgggtgaacaagaaagagtgtatagcattgttgttcaattcagtattaatagataatgtaactactgtagGTACAAAGGTTTCCATGACTATGCAAAATTGAAAGGAGTGGATGTTGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAG
upper sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 3
gtaaggggtttcgtttggagctttggtgtctatcaggaactgagagatctcaatattttttgtccctgag----------ttgcctttgattcattacagGTACAAAGGATTTCATGAGTATGCAAAGTCAAAAGGTGTGAATCTTGGTTCACCAGTTGGACTTGATGTGCTTGTTGATGGAATTGTTCCTACAG
||| |||| | | | ||| || | | ||| || ||||| | | | ||| | | |||||||||||||| | | |||| ||||| || | |||||| || || ||||| |||||||||||||||||| ||| ||||||| | ||||||||||
ataattagtttacctctccattactttaataggttggactcgaattttgttaatgttgcttgtcaccggaaattaatggttcatcttctacactctacagGTACAAAGGTTATTATGAATATGCTAAATTAAAAGGAGTTGATGTTGGTGTACCAGTTGGACTTGATGTCCTTATTGATGGCACGGTTCCTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaactgagagatctcaatattttttgtccctgagttgcctttgattcattacagGTACAAAGGATTTCATGAGTATGCAAAGTCAAAAGGTGTGAATCTTGGTTCACCAGTTGGACTTGATGTGCTTGTTGATGGAATTGTTCCTACAG
ctttgat putative branch site (score: 5)
atctcaatatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggggtttcgtttggagctttggtgtctatcaggaactgagagatctcaatattttttgtccctgagttgcctttgattcattacagGTACAAAGGATTTCATGAGTATGCAAAGTCAAAAGGTGTGAATCTTGGTTCACCAGTTGGACTTGATGTGCTTGTTGATGGAATTGTTCCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA