Sequence
atgc intronic sequence ATGC exonic sequencegtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattgttaactgttaatataacttgaatataattttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04190.4 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04190.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G153704_T02 (Zea mays), 3'ss of exon 12
gtaagtggtt-tg--tcatacgctttagtcaggccttttgctgattgtcattgttaactgttaatataacttgaatata--attttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCT
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gtaagttgtcatgattcatcctgtttgttctgattctatttgaatgtataacttcaatgtttgacatgactggagtatatgattctgtgcagGTACGTGCTGTCATTTGCTCTAGGAGCGGGCCCTGTTCCAGCGCTACTTCTTCCTGAAATATTTGCCTCGAGAATAAGGGCCAAGGCTGTCGCATTATCT
upper sequence: LOC_Os01g04190.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 12
gtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattg------ttaactgttaatataacttgaatataat-tttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCT
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gtaagttgttaatgattcatcttgtttggtc--tttgctgattctatttaaatgtataacttgaatgtttgacataactggagtatttgtgcagGTATGTGCTGTCTTTTGCTCTAGGAGCTGGTCCTGTTCCTGCCCTGCTTCTTCCTGAAATATTTGCCTCCAGAATAAGGGCCAAGGCTGTTGCATTATCT
upper sequence: LOC_Os01g04190.3 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 12
----------------------gtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattgt-taactgttaata--taacttgaatataattttatttagG----TATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCT
| || | |||| | | || || ||| | || || | |||| ||| | | | ||| || ||||| | |||||| |||| || ||||||| ||||| || || || || | || ||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||
gtaagttgatacttttccttatcatattgatgtgtcttttctctctaccaatccatttcttctttttcccaatctaacccaggatacttgaacttgctatctttccatttatgcagCTATGTGTTGTCCTTCTCTCTTGGTGCTGGTCCTGTCCCTGCTCTTCTTCTTCCAGAAATATTTGCCTCTAGAATCAGGGCAAAAGCAGTTGCTTTATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgctgattgtcattgttaactgttaatataacttgaatataattttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCT
ttttattt CT-rich tract
attgttaactgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtggtttgtcatacgctttagtcaggccttttgctgattgtcattgttaactgttaatataacttgaatataattttatttagGTATGTGCTGTCTTTTGCTCTTGGAGCTGGCCCAGTTCCAGCATTGCTCCTTCCTGAAATATTTGCCTCCAGAATAAGGGCTAAAGCTGTTGCATTATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT