Sequence
atgc intronic sequence ATGC exonic sequencegtcagatcatgtttgatatgattttattcttccatggaaaataattacatttttaataagctaacagagttggttgcatcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g24220.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G421541_T02 (Zea mays), 3'ss of exon 6
gtcagatcatgtttgatatgattttattcttccatggaaaataattacatttttaataagctaacagagttggttgcatcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
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------gtaaactt-atttaatgtttttcctcattaaatttcacacataattgcattttagcaataacattaattgcattacagGGTTATCGAGTTCTGGTTGTCGAGCAAACTGAAACACCTGACCAGCTTGAACTTCGGCGTAAGGAGATGGGTATAAAGGACAAG
upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gtcagatcatgtttgatatgattttatt-cttccatggaaaataattacattttta------ataagctaacagagttg--gttgcatcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
|| |||| | |||| | ||| ||| | || | | || | | || || |||| | | ||||||||||||||||| ||| | ||||||||||| ||||| || ||||| || || || || || || | || ||||| |||
gtttgtctcacaaatgactccccccccccccccccccccccctcttttcatctcagatacagactaattacttgtctaacaagccaacctgtaactaggggggaggaacttactaagtttccatggttgagcagGGTTATCGAGTTCTTGTTGTAGAGCAGACTGATACACCTGAACAGCTGGAGCTTCGTCGCAAGGAGAAGGGCTCTAAAGATAAG
upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtcagatcatgtttgatatgattttattcttccatggaaaataattacatttttaataagctaacagagttggttg--catcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
| || ||| | |||| | ||| | || ||| ||| || ||| | ||| || ||||||||||| ||||| ||| | ||||| || |||||||| ||||||||||| || || || ||||| | ||| || ||||||
gttgatcctattacatattttctatctcaaattagaattgttttccattggctttagagcacctctatttctttcatgaacccattttcatcaagaattc-ttactggagctccttggacagtgcagGGTTATCGTGTTCTTGTTGTAGAGCAAACAGAAACACCTGAGCAGCTTGAGCTTCGTCGCAAAGAGAAGGGTTCTAAGGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccatggaaaataattacatttttaataagctaacagagttggttgcatcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
agctaac putative branch site (score: 2)
aaaataattacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagatcatgtttgatatgattttattcttccatggaaaataattacatttttaataagctaacagagttggttgcatcacagGGTTATCGAGTTCTGGTTATCGAGCAGACTGAAACACCGGAGCAGCTTGACCTCCGCCGTAAAGAAACTGGTGTAAAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA