Sequence
atgc intronic sequence ATGC exonic sequencegtgagctataacccctttttttgttgcagtacagtaatcaaagtaaaactcgattctgatgtcacttgttttgcttccacagAATCTTGATGCAGAGGCTTTGCAATGTTGATCCAAGTTTTCTGACGAACAAGCAGAAGCTGGCGTTCTGGATTAACATCTACAACTTCTGCATAATGCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g05480.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g05480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G030712_T02 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------gtgagctata--acccctttttttgttgca----gtacagtaatcaaagtaaaactcgattctgatgtcacttgttttgcttccac--agAATCTTGATGCAGAGGCTTTGCAATGTTGATCCAAGTTTTCTGACGAACAAGCAGAAGCTGGCGTTCTGGATTAACATCTACAACTTCTGCATAATGCAT
| || || || ||| | || | | | | | | | | || | || | || | | ||| | ||||||||| ||| ||| || || || || || ||||||||||||||||||||||||| ||||| ||| |||||||||||||| | ||||||
gtgcgtgcgcttgagctgacgggctccccgcctcccccccagtttgtgtcgtgtgcaactgtgcatgctgcttgctgcctgtacagcctcttgactgactgaatgatggatggcttttgttttggcctccctgtatgcgtctgcgtgcgtgcctactgcctagAGGCCTGATGCAGAAGCTCTGCGCCGTCGACCCCAGCCTTATGACGAACAAGCAGAAGCTGGCGTTTTGGATCAACGTCTACAACTTCTGCGTGATGCAT
upper sequence: LOC_Os01g05480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G07390.1 (Glycine max), 3'ss of exon 4
--------------gtgagctataacccctt-----tttttgttgcagtacagtaatcaaagtaaaactcgattctgatgtcacttgttttgcttccacagAATCTTGATGCAGAGGCTTTGCAATGTTGATCCAAGTTTTCTGACGAACAAGCAGAAGCTGGCGTTCTGGATTAACATCTACAACTTCTGCATAATGCAT
| | ||||| || || | || |||| | || | ||| || | ||| || || ||| | || | |||||||| | ||| || |||||||| |||||| |||| ||||||||||| |||| |||||||| ||||||||||| |||||||||| ||
gactttcacttcgcaacaccaataactatttaaacattgtctacatgttatagtataacatgttatactatcttttagc-tcattttttcctcttttatagGGTGTTGATGCATAAGCTATGTGATGTTGATTTAAGTTTCTTGACATACAAGCAGAAGTTGGCATTCTGGATCAACATCTACAATGCCTGCATAATGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtacagtaatcaaagtaaaactcgattctgatgtcacttgttttgcttccacagAATCTTGATGCAGAGGCTTTGCAATGTTGATCCAAGTTTTCTGACGAACAAGCAGAAGCTGGCGTTCTGGATTAACATCTACAACTTCTGCATAATGCAT
ttctgat putative branch site (score: 3)
cttgttttgcttcc putative PPT
taatcaaagtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctataacccctttttttgttgcagtacagtaatcaaagtaaaactcgattctgatgtcacttgttttgcttccacagAATCTTGATGCAGAGGCTTTGCAATGTTGATCCAAGTTTTCTGACGAACAAGCAGAAGCTGGCGTTCTGGATTAACATCTACAACTTCTGCATAATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG