Sequence
atgc intronic sequence ATGC exonic sequence...tgttgtatagagatctttacctactgatgttgtcagtgctacttgataggggtttaatgattttaaactcattagtttctctcaatttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G14120.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 9
tgttgtatagagatctttacctactgatgttg---tcagtgctacttgatagg---ggtttaatgattttaaactcattagtttctctcaat-ttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
||| | | | || | | | ||| || || || | | | ||| | | |||| || ||| | || ||||||| ||||| ||||||||| |||| | |||||| || || ||||| ||||| ||||| ||||| |||| ||| ||||| |||||||||||
----atatgcgattacccaatcgtttatatggcgttgagttttaagcaattggcaaaatgtgctaattccttgccttattgtttaacttaatgctatcatgcagGAGGTGGATCCGTGTGAAGACCTAACTGATGATGACATCCGTACTGCCATACAGAATGCTACTGGGCCCAAATCAGCATTGTTTGTTCCAGAA
upper sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 9
-tgttgtatagagatctttacctactgatgttgtcagtgc--tacttgataggggtttaatgattttaaactcattagtttctctcaatttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
| || || | | | || || | | ||| | | | ||| | | || | | | ||| | ||||||| |||||||||||||| || || | |||||||||||| || || ||||| ||||| ||||| || | ||| ||| | |||||||||||
tcactccattgaaccacccaatgatcatgttcctctgttcatttcttcaatgctagctcctgagtcctattatataatgcaataaaattttatcttacagGAGGTGGATCCATGTGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCCACTGGACCTAAATCAGCACTGTTTGTTCCAGAA
upper sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 9
-tgttgtatagagatctttacctac--tgatgttgtcagtgctacttgataggggtttaatgattttaaactcattagtttctctcaatttgctctga-aggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
| || || | | || || | | | ||| | | | ||| | | || | | | ||||| ||| | ||||||| |||||||| ||||| || || | |||||||||||| || || ||||| ||||||||||| || | ||| ||| | |||||||| ||
tcactccattgaaccacccaatgatcatgttgctctgttcatttcttcaatgctagctcctgagtcctattatat-aatgcaattaaattttatctaacagGAGGTGGATCCATGCGAAGATTTGACTGATGATGATATTCGCACAGCCATACAGAATGCAACTGGACCTAAATCAGCACTGTTTGTTCCTGAA
upper sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 9
---tgttgt-atagagatctttacctactgatgttgtcagtgctacttgataggggtttaatgattttaaactcattagtttctctcaat-ttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
||| | | | |||| | || || | || | ||| | | | | ||| | | |||| || ||| | || ||||||| ||||| ||||||||| | || | |||||| || || ||||| ||||| ||||| ||||| |||| ||| || || |||||||||||
atatgtgattacccaatggtttatatggtgttgagttttaagcaa-ttggcaaaa-tgtgctaattccttgccttattgtttaacttaatgctatcatgcagGAGGTGGATCCGTGTGAAGACCTGACTGATGATGACATCCGTACTGCCATACAGAATGCTACTGGGCCCAAATCAGCGTTGTTTGTTCCAGAA
upper sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 9
tgttgtatagagatctttacctactgatgttgtc-agtgctacttgatagg---ggtttaatgattttaaactcattagtttctctcaat-ttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
|| | | | || | ||| ||| ||| || ||||||| | | | ||| | | || | || ||| | |||||||||| ||||| ||||||||| | || | ||| || ||||| ||||| ||||||||||| ||||| || | ||| ||| | |||| |||| |
--ttttgttattgcttgtatggttttatggtgttgagttttatgtgataggcaaaatgtgctaattccttgccttgttgtgtaacttaatgctatcatgaagGAGGTGGATCCGTGTGAAGACCTGACTGATGACGACATTCGTACTGCCATACAAAATGCTACTGGACCTAAATCAGCAGTGTTTGCTCCATCT
upper sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 10
tgttgtatagagatctttacctactgatgttgtcag---tgctacttgataggggtttaatgattttaaactcatta-gtttctctcaatttg-----ctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
|| |||| | | || | | ||| | || | ||| || | | | | ||||| | || | ||||| || || ||||||| ||||||||||| || || || | |||||| ||||| |||||||| || |||||||| || || ||||||||||||||||| |||||
------atggagaacctcacaattttttattggtaaatctgatgtttgctaatttcagagctgctatgagctcatcaagtctgaggagatttgaatatctgtgcagGAGGTGGATCCATGTGAGGATTTGACTGATGATGACATTCGAACTGCAATTCAGAATGCAACCGGCCCTAGATCTGCATTATTTGTGCCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataggggtttaatgattttaaactcattagtttctctcaatttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
gtttaat putative branch site (score: 4)
tttgctct putative PPT
tttaatgattttaaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgtatagagatctttacctactgatgttgtcagtgctacttgataggggtttaatgattttaaactcattagtttctctcaatttgctctgaaggagGTTGATCCATGTGAAGACTTAACAGCTGATGATATTCGGACTGCAATACAAAATGCAACTGGTCCCAGATCTGCATTATTTGTTCCAGAT
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