Sequence
atgc intronic sequence ATGC exonic sequencegtactagcagaataagatgttctattcttcattccactaaatcaatttgctaattgtattacatatatcagGTCTGATCGGATGGCACAGCTTCTAGATGAGCGGGATCTGGGCGTACTGACATCTGTCATGAGCCTTTTTGTTTCACTGGTATCTAATAATGCTGAAGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02150.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 5
------------------------gtactagcagaataagat--gttctattctt---cattccactaaatcaatttgctaattgtattacatatatcagGTCTGATCGGATGGCACAGCTTCTAGATGAGCGGGATCTGGGCGTACTGACATCTGTCATGAGCCTTTTTGTTTCACTGGTATCTAATAATGCTGAAGCA
| |||| | | | ||| ||||| || || ||| ||| ||| |||| ||| ||| |||||||| ||||||| |||||||| |||||||||||||| ||||| || || ||||||||||||||||| |||||||||||||| ||||| || ||| ||||||||
tcagtggaaaggcttctcaccactgcgctaggcctgtcatttttgttacattctgttacactctacttaattaataggctacttgaattctgcatatcagGGCTGATCGAATGGCACAACTTCTAGATGAGCGTGATCTAGGTGTGCTGACATCTGTCATGAGTCTTTTTGTTTCACTAGTATCCAACAATTCTGAAGCA
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 6
gtactagcagaataagatg--ttctatt------cttcattccactaaatcaatttgctaattgtattacatatatcagGTCTGATCGGATGGCACAGCTTCTAGATGAGCGGGATCTGGGCGTACTGACATCTGTCATGAGCCTTTTTGTTTCACTGGTATCTAATAATGCTGAAGCA
||| || | ||| || ||||||| | | || ||| ||||||| |||||| | ||| ||||||||| |||| || |||||||| |||||||||||||| ||| | || || ||||||||||||| ||| |||||||||||||| ||||| || |||| |||||||
gtagtaaaattatagaatacattctattatagtattatactctacttaatcaataggctaatcgaattctgtatatcagGGCTGACCGAATGGCACAACTTCTAGATGAGCGTGATTTAGGTGTGCTGACATCTGTCACGAGTCTTTTTGTTTCACTAGTATCCAACAATGTTGAAGCA
upper sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------gtactagcagaata-agatgttctattcttcattccactaaa--tcaatttgctaattgtattacatatatcagGTCTGATCGGATGGCACAGCTTCTAGATGAGCGGGATCTGGGCGTACTGACATCTGTCATGAGCCTTTTTGTTTCACTGGTATCTAATAATGCTGAAGCA
| | | | || | | ||| | | | | | | | | | | | | | | | ||||||| ||||||||||| |||||| ||||||| || |||||||| || |||||||| ||||||||| ||||| | | ||||| || || ||| |||
cttcttgtttcattatgaaatgggcattctttgaaacatgtgggttgcctaagatgtgtcctatttatgcttaggtgattctcttttgcaaacctttcagGTCAGATCGGATGGCGCAGCTTTTAGATGAACGTGATCTGGGTGTCTTGACATCTTCAATGAGCCTTCTTGTTGCTTTAGTATCAAACAACCATGATGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttctattcttcattccactaaatcaatttgctaattgtattacatatatcagGTCTGATCGGATGGCACAGCTTCTAGATGAGCGGGATCTGGGCGTACTGACATCTGTCATGAGCCTTTTTGTTTCACTGGTATCTAATAATGCTGAAGCA
tgctaat putative branch site (score: 2)
taattgtattacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactagcagaataagatgttctattcttcattccactaaatcaatttgctaattgtattacatatatcagGTCTGATCGGATGGCACAGCTTCTAGATGAGCGGGATCTGGGCGTACTGACATCTGTCATGAGCCTTTTTGTTTCACTGGTATCTAATAATGCTGAAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC