Sequence
atgc intronic sequence ATGC exonic sequence...accatttttcagcaaatgatactgaaattaatgctgactggtttcatctgtgaaatgtattgattgaaaaccttgtcacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66890.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66890.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G807064_T01 (Zea mays), 3'ss of exon 3
accatttttcagcaaatg---atactgaaattaatgctgactggtttcatctgtgaa-atgtattgattgaaaaccttgtcacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
| | || | || || || | | |||||| | || | || | | | |||| | || ||| |||| ||||| ||||||||| | ||||||||| | | | || ||| ||||||| ||||||||||| ||||| || || |||||||||| |||||| || |||||||
----tgatgaagacagtgcagattcttcttcttcttctgacttttgatgcgtgcgtgcatctttcagtgagaaacagacgcgctgaattatttgtttggtgaagGTTTGAGCAGGAACAGATGAAGGAGCACGCTCTGCATTTGCTTGTGCTCTCCCACGTCTTCTCGGTGCCGTCTCTGAAGACGGTCTGCGTCGACCAACTC
upper sequence: LOC_Os01g66890.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G475663_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------accatttttcagcaaatgatactga---aattaatgctgactggtttcatctgtgaaatg--tattgat-------------------tgaaaaccttgt-cacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
| || ||| ||| | ||| |||| | | ||| || | | | | | ||| | ||||| ||| || | | || | ||| |||| ||||| ||||||||| | ||||||||| | | | || ||| ||||||||||||||||||| ||||| || || |||||||||| || ||| || |||||||
gtatggatgctatctactcattcgtttagatagttcactgtcctctaattctctaaagatcagatttcagcccaaacagtttacagtgactgaagctgatgaagacagtgcagattcttcttcttcttctgatgacttttgatgtgtgcgtgcatctttctgtgagaaacagacgcgctgatttatttgtttggtgaagGTTTGAGCAGGAACAGATGAAGGAGCACGCTCTGCATTTGCTTGTACTCTCCCACGTCTTCTCGGTGCCGTCTCTGAAGACGGTTTGCGTCGACCAACTC
upper sequence: LOC_Os01g66890.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G479736_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------------------------accatttttcagcaaatgatactgaaattaatgctgactggtttcatctgtgaa-atgtattgattgaaaaccttgtcacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
| | ||| || | || ||||| ||||| | | |||| || | | | |||| | || | ||| |||| ||||| ||||||||| | ||||||||| | | | || ||| ||||||||||||||||||| ||||| || || |||||||||| |||||| || |||||||
gtatggatgctatctactcattcgtgtagatagttcactgtcctctaattctctaaagatcagatttcagcccaaacagtttacagtgactgaagctgatgaagacagtgcagattcttcttcttctaatgatgacttttgatgtgtgtgtgcatctttcagtgagaaacagacgcgctgatttatttgtttggtgaagGTTTGAGCAGGAACAGATGAAGGAGCACGCTCTGCATTTGCTTGTACTCTCCCACGTCTTCTCGGTGCCGTCTCTGAAGACGGTCTGCGTCGACCAACTC
upper sequence: LOC_Os01g66890.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G082666_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------accatttttcagcaaatgatactga---aattaatgctgactggt----ttcatctg--------tgaaatgta---------ttgattgaaaaccttgt-cacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
| || ||| ||| | ||| |||| | | ||| || | | ||| |||| ||| ||| || | ||| || | | || | ||| |||| ||||| ||||||||| | ||||||||| | | | || ||| ||||||||||||||||||| ||||| || || |||||||||| |||||| || |||||||
gtatggatgctatctactcattcgtttagatagttcactgtcctctaattctctaaagatcagatttcagcccaaacaatttacagtgactgaagctgatgaagacagtgcagattcttcttcttcttctgatgacttttgatgtgtgcgtgcatctttcagtgagaaacagacgcgctgatttatttgtttggtgaagGTTTGAGCAGGAACAGATGAAGGAGCACGCTCTGCATTTGCTTGTACTCTCCCACGTCTTCTCGGTGCCGTCTCTGAAGACGGTCTGCGTCGACCAACTC
upper sequence: LOC_Os01g66890.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G055175_T01 (Zea mays), 3'ss of exon 2
accatttttcagcaaatgatactgaaattaatgctgactggtttcatctgtgaa-atgtattgattgaaaaccttgtcacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
| ||| || | || | || ||||| | | || | || | | | |||| ||| | | ||| |||| ||||| ||||||||| | ||||||||| | | | || ||| ||||||||||||||||||| ||||| || || |||||||||| |||||| || |||||||
-tgaaaacagtgcagattcttcttcttcttctgatgacttttgatgtgtgcgtgcatctttcagtgagaaacagacgcacatatttatttgtttggtgaagGTTTGAGCAGGAACAGATGAAGGAGCACGCTCTGCATTTGCTTGTACTCTCCCACGTCTTCTCGGTGCCGTCTCTGAAGACGGTCTGCGTCGACCAACTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgtgaaatgtattgattgaaaaccttgtcacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
tattgat putative branch site (score: 3)
cttttattt putative PPT
ttttatttgttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatttttcagcaaatgatactgaaattaatgctgactggtttcatctgtgaaatgtattgattgaaaaccttgtcacttgtgcttttatttgttgaagTTTTGAGCAGTATCAGATGAAGAGGTATGTACTTCATCTGCTTGTACTCTCCCACGTTTTCTCAGTACCATCTCTGAAGAGAGTCTGCATCAACCAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA