Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgatgacactttttcaatctctccagattgctaatctatttggttgaaacttgaaagtaaaggtttgtttttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32850.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g37880.3 (Oryza sativa), 3'ss of exon 4
-----gtatgtgatgacactttttcaatctctccagattgc----taatctatttggttgaaacttgaaagtaaaggtttgttt--ttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
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tgttcttaatttttgaaatctatatattcatcctgcaatgcattatattcaaaccaaggtgaatttgtttataaaatttttttgaattgacatttggcagGCCTTGGGGTGCCTTCTATATAGAATATGCTACTTCAAGTCTGCATTTGATGGAGAGTCCAAGTTGCAGATACTTAATGGCAATTATCGTATTCCAGAGC
upper sequence: AT2G32850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G416684_T01 (Zea mays), 3'ss of exon 2
---------gtatgtgatgacactt--tttcaatctctccagattgctaatctatttggttgaaacttgaaagtaaaggtttgtttttaaaaaaaa---atagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
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gcaaatgttgcctatcatattattgaattgcaatttttttgtactgattaaatact-aatagtgccatga--gttaacattagtgtttgtgatttttttacagGCTCTTGGGTGTCTCTTGTATAGAATTTGCTACTTCAAATCAGCATTTGATGGAGAATCAAAGCTCCAAATACTTAACGGGAACTATCGCATCCCAGAAT
upper sequence: AT2G32850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G42460.1 (Glycine max), 3'ss of exon 5
-------------gtatgtgatgacactttttcaatctctccagattgctaatctatttggttgaaacttgaaagtaaaggtttgtttttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
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gtaagtcatctatgcctaaaacttatctttttaattatataaatatttgccatatctttctatgctagttgtggaatcatattacttgttgaatatt--tagGCACTTGGATGTCTCCTTTTTCGCATATGCTACTTCAAAAGTGCTTTTGATGGGGAATCAAAGCTCCAAGTCTTAAATGGAAACTACCGCATTCCCGAAT
upper sequence: AT2G32850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G15920.1 (Glycine max), 3'ss of exon 5
-------gtatgtgatgacactttttcaatctctccagattgctaat--ctatttggttgaaacttgaaagtaaaggtttgtttttaa--aaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
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gtaagtcatgcatgcctaaacctcatctttttaattatataaatatttgccaaatctttctatgctaattgaggaatcatattactgattgaatacatagGCTCTTGGGTGTCTCCTTTTTCGCATATGCTACTTCAAAAGTGCTTTTGATGGGGAGTCAAAGCTCCAAGTCTTAAATGGAAACTACCGCATTCCTGAAT
upper sequence: AT2G32850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0156g00640.t01 (Vitis vinifera), 3'ss of exon 5
----------------------gtatgtgatgacactttttcaatctctccagattgctaatctatttg-gttgaaacttgaaagtaaaggtttgtttttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
| | |||| || | | | | | | || | | || | | | || ||| | || | |||| ||||| || ||| | ||||| |||||||| ||||| |||||||||||| ||||||||| | ||||||||||| || || || || ||||||||||
gtaagtcagttatactttatttttgttcaatgagtctgggttatgatttgctattcaagaagttttctgtgctttttaatacaaccaaaacctgaaattcatctttttgcagGCGCTTGGGTGCCTCCTCTTTCGCATATGCTACTTCAAATCTGCATTTGATGGTGAATCAAAGTTACAAATCTTAAATGGAAACTACCGCATTCCAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctaatctatttggttgaaacttgaaagtaaaggtttgtttttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
tgctaat putative branch site (score: 2)
aaagtaaaggtttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgatgacactttttcaatctctccagattgctaatctatttggttgaaacttgaaagtaaaggtttgtttttaaaaaaaaatagGCTCTTGGATGTCTCTTGTTTCGGATATGCTATTTCAAGAATGCATTTGATGGAGAATCAAAGCTGCAAATCTTAAACGGGAATTATCGTATTCCAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC