Sequence
atgc intronic sequence ATGC exonic sequencegtattttttgtcgaagttgtttttctgattaacgttttcatttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20000.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G51450.1 (Glycine max), 3'ss of exon 12
-------------------gtattttttgtcg--aagttgtttt--tctgattaacgttttcatttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
||| || | |||| | |||||||| || |||||| | | ||| | | | | | | | | |||||||| ||||| |||||||||||| |||||||||| ||||| || |||||||||||||| | ||||||||||||||||||||| |||||||||||||||
aagtatatttatatcattaacattacctgctatttggctgttctattctgatta---ttatcattttatctgggt--ttataattgtggtcgaatgctctggcagGTGTGCCATGGGTAATTGCTATAGCCTGCAAAAGGATCATGAAACTGCACTGAAGAATTTTCAACGAGCTGTTCAACTGAATCCCAGATTTGCATATGCA
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G28550.1 (Glycine max), 3'ss of exon 12
----------------------gtattttttgtcgaagttgttt-ttctgattaacgttttcatttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
|| | | | || | | ||||||||| || ||||| | | ||| | | | | | | |||||||||| ||||| |||||||||||| |||||||||| ||||| || |||||||||||||| | ||||||||||||||||||||| | |||||||||||||
aaagtatatttatatcataacattacctgctatttggcttatctattctgatta---ttatcattctatctgggt--ttataattttggttgaatgctctggtagGTGTGCCATGGGTAATTGCTATAGCCTGCAAAAGGATCATGAAACTGCACTGAAGAATTTTCAACGAGCTGTTCAACTGAATCCCAAATTTGCATATGCA
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G07140.1 (Glycine max), 3'ss of exon 14
------------gtattttttgtcgaagttgtttttctgattaacgttttcat--ttattgttggtaataagagaaataagcaatcaattat----gtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
| || | ||| | || | |||| || || | | | | | | | | | || | |||||||| ||||| |||||||| || | || || || ||||| || |||||||||||||| | ||||||||||||||||||||| |||||||||||||||
agagttgaacattccccccctcccggggctgtatatcgctgttctattttaatcattgtcacttatcctggtttatcttttctgtttaataccgtggcagGTGTGCCATGGGTAATTGCTACAGTCTACAGAAAGATCATGAAACTGCACTGAAGAATTTTCAACGAGCTGTTCAACTGAATCCCAGATTTGCATATGCA
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G05640.1 (Glycine max), 3'ss of exon 12
------------------gtattttttgtcgaagttgtttttctgattaa--cgttttcatttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
| | ||| | |||| || | || ||| |||| |||| || | ||| | | | |||||||| ||||| |||||||| || | || || || ||||| || |||||||||||||| | ||| ||||||||||||||||| |||||||||||||||
gagagttgaaccccccccaccccccacttgtattttgctgttctattttaattattgtcacttatc-ctggttttatcttttctgttgaat-actgtggcagGTGTGCCATGGGTAATTGCTACAGTCTACAGAAAGATCATGAAACGGCACTGAAGAATTTTCAACGGGCTGTTCAACTGAATCCCAGATTTGCATATGCA
upper sequence: AT2G20000.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv11s0016g03260.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------------------------------------------------------------------------------gtattttttgtcgaagttgtttt------tctgattaacgtttt-catttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
| || | ||| || || | | |||| | | | | ||| | || | ||| || ||| |||||||| ||||||||||||||||| ||||| || |||||||| || || || |||||||||| || || || ||||| ||| ||||||||||||||||
gtaggttattaacttctgtaatataatacagcactaactttcagctgatagaaaatgtctgtcaaacagggttgtttcaccaccttatttttcatggtcatttttgtctgttacagctgcactgaaggtttcaattattgctctatgaacttcgttcatcttatcttttctgttaaatggat-atgcagGTGTGCCATGGGAAATTGCTATAGTTTGCAGAAAGACCATGAAACTGCTCTAAAGAATTTCCAGCGTGCAGTGCAACTAAATTCAAGATTTGCATATGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaacgttttcatttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
gattaac putative branch site (score: 2)
ttttcatttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttttgtcgaagttgtttttctgattaacgttttcatttattgttggtaataagagaaataagcaatcaattatgtagGTGTGCTATGGGAAATTGCTATAGCTTGCAAAAGGACCATGAGACCGCACTGAAGAATTTCCTACGAGCTGTTCAACTGAATCCAAGATTTGCATATGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT