Sequence
atgc intronic sequence ATGC exonic sequence...tgtgactctttgttttttttttttgatggcatgctaaccttggatgtctttgcttctgttttttcactgaatagtttctctatatgtcttgttgctgcagGCACCCAACATCACTTCATGACCATGGTAGGGATAGTGATGATGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os01g40390.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G812498_T01 (Zea mays), 3'ss of exon 5
---------------tgtgactctttgtttttttttt---ttgatggcatgctaacc--ttggatgtctttgcttctgttttttcactgaatagtttctctatatgtcttgttgctgcagGCACCCAACATCACTTCATGACCATGGTAGGGATAGTGATGATGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAG
| ||| || || || | | || || | || | ||| ||| | || | | ||| | | ||| ||| |||| || | ||||||| | |||||||| || ||||| | ||| |||||||| ||||| || || ||||||||||| || || ||||||||||| || ||||||| ||||||||
gtatgttcttccattctgggttctctgattattgtctacactgctgaaacacttgtcatttgtctgtggtaaattttatatttcttcctgactgttgg-cta-atgttttat-gctgcagCCGTCCAACATCTCTACATGATCGTGGGAGGGATAGCGATGACGACGACTTCCGAGACAGAGACTACGATGTGGCAGCACTCACTAATAATATGAGCCAG
upper sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 15
tgtgactctttgttttttttttttgatggcatgctaaccttggatgtctttgcttctgttttttcactgaatagtt-tctctatatgtcttgttgctg-cagGCACCCAACATCACTTCATGACCATGGTAGGGATAGTGATGATGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAG
| ||||| | | || | | | || | | | || | | | || || || | | ||| | ||| | | |||| || || ||||| ||||| | | |||| ||||||||||||||||||| || || || ||||||||||||||||| || || || || |||||||||
-gaagttctttagggggtgataaatattatttatgagaggcagtagtgatggttggtgcagtat-atggattaattctttttattgatattgctcttaacagGAGGCCTACTTCACTCCATGATCGTAGTAGAGATAGTGATGATGATGATTACCACGATAGAGATTATGATGTGGCAGCCCTAGCAAACAATTTGAGCCAG
upper sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 15
tgtgactctttgttttttttttttgatggcatgctaaccttggatgtctttgcttctgttttttcactgaatagtttctctatatgtctt--gttgctgcagGCACCCAACATCACTTCATGACCATGGTAGGGATAGTGATGATGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAG
| | || | | | | | || | ||| || | | | |||| ||| | ||| | || | ||| |||| || ||| | || || || | ||||||||||||||||||||||| | |||||| ||||||||||| |||||||| || ||||||||||| |||
--aaattagagaaccaattactatattaacgtaatagaaaatggtgttatttcccccctcttttggtctgatatgtaatctgagtttcatcaattgtaacagGAGACCTACAGCTCTACAGGATCGAACTAGGGATAGTGATGATGATGATTATCAAGACAGAGATTATGATGTTGCAGCTCTAGCAAATAACTTGAGTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctttgcttctgttttttcactgaatagtttctctatatgtcttgttgctgcagGCACCCAACATCACTTCATGACCATGGTAGGGATAGTGATGATGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAG
tcttgtt CT-rich tract
tgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgactctttgttttttttttttgatggcatgctaaccttggatgtctttgcttctgttttttcactgaatagtttctctatatgtcttgttgctgcagGCACCCAACATCACTTCATGACCATGGTAGGGATAGTGATGATGATGATTTCCGAGACAGGGATTATGATGTGGCAGCTCTTGCTAATAACTTGAGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - -ggcatgc
- - - - - - - - - - - - - - - - - - - -ttggatg
