Sequence
atgc intronic sequence ATGC exonic sequence...catttgaggaagtagcatgaactaccaatggtttctatgcatcctatctgtacagtatggtgatatcaccgagttaatgaattgttgacactccaaacagTCATCCTTCCTTTGGGGTTATCTGGTGTCACCAATAATTGGTGGAGCACTGGTCGACTACTATGGCGGAAAGCGAGTTATGGCTTATGGCGTGGCTCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g63290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g63290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G856598_T02 (Zea mays), 3'ss of exon 1
-----catttgaggaagtagcatgaactaccaatggtttctatgcatcctatctgtacagtatggtga-tatcaccgagttaatgaattgttgacactccaaacagTCATCCTTCCTTTGGGGTTATCTGGTGTCACCAATAATTGGTGGAGCACTGGTCGACTACTATGGCGGAAAGCGAGTTATGGCTTATGGCGTGGCTCTAT
| ||| ||| | | | | || ||| | | | | | | || ||| ||| | | || || ||| |||| ||||||||||||||| |||||||| |||||| |||| || ||||||||||||||||| || || ||||| || ||||| ||||| |||||||| || || ||
tgaagtaaatgatgaaaaattacacataagaaagtaagggcatg-agcttgcccatcttatttgatgaatattctgatgccattgtgtt-ttgtcactgcaaACAGTCATCCTTTCTTTGGGGATATCTGATGTCGCCGATAATTGGTGGAGCACTTGTTGATTACTACGGTGGAAAACGAGTCATGGCTTACGGTGTAGCA----
upper sequence: LOC_Os01g63290.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G856598_T01 (Zea mays), 3'ss of exon 1
-catttgaggaagtagcatgaactaccaatggtttctatgcatcctatctgtacagtatggtga-tatcaccgagttaatgaattgttgacactccaaacagTCATCCTTCCTTTGGGGTTATCTGGTGTCACCAATAATTGGTGGAGCACTGGTCGACTACTATGGCGGAAAGCGAGTTATGGCTTATGGCGTGGCTCTAT
| ||| ||| | | | | || ||| | | | | | | || ||| ||| | | || || ||| |||| ||||||||||||||| |||||||| |||||| |||| || ||||||||||||||||| || || ||||| || ||||| ||||| |||||||| || || || |||
gtaaatgatgaaaaattacacataagaaagtaagggcatg-agcttgcccatcttatttgatgaatattctgatgccattgtgtt-ttgtcactgcaaacagTCATCCTTTCTTTGGGGATATCTGATGTCGCCGATAATTGGTGGAGCACTTGTTGATTACTACGGTGGAAAACGAGTCATGGCTTACGGTGTAGCATTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgtacagtatggtgatatcaccgagttaatgaattgttgacactccaaacagTCATCCTTCCTTTGGGGTTATCTGGTGTCACCAATAATTGGTGGAGCACTGGTCGACTACTATGGCGGAAAGCGAGTTATGGCTTATGGCGTGGCTCTAT
tgttgac putative branch site (score: 3)
ttaatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catttgaggaagtagcatgaactaccaatggtttctatgcatcctatctgtacagtatggtgatatcaccgagttaatgaattgttgacactccaaacagTCATCCTTCCTTTGGGGTTATCTGGTGTCACCAATAATTGGTGGAGCACTGGTCGACTACTATGGCGGAAAGCGAGTTATGGCTTATGGCGTGGCTCTAT
- - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttga