Sequence
atgc intronic sequence ATGC exonic sequence...ccaaacatcctaatattttgatgtgtttttactttacttgtttgcattatatccatagtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60700.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G380227_T02 (Zea mays), 3'ss of exon 3
ccaaacatcctaatattttgatgtgtttttactttacttg-tttgcattatatccat--agtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
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---agttaacaagaatatatgtataatattgtgatataaaacctgcaccatacctgttaattaatcgacgtcatgttgtccactagagatttgttttcttcagTCTGCAGCAAACCTTTCGGTGGAGACCTTGGAGAAGGGTTTACTCACTCCCAAGAGCAATGTCTGGAGCTTTGGAGTCGTGTTACTGGAGCTAATAACTA
upper sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G871928_T01 (Zea mays), 3'ss of exon 2
-------------ccaaacatcct-aatattttgatgtgtttttactttacttgtttgcattatatccat--agtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
|| | | ||||| | || || | | || |||| ||| | | | | || | | ||| | | | | || | | || | || |||| |||||||| || ||||| ||||||||||| ||| |||| ||||||||||| || |||||| |||||||||| | | |
aagtaacattgggtcagttaacaagaatatatgtataatattgtgatataaa-acctgcaccatacctgttaattaatcgacgtcatgttgttcactagagATTTGTTTTCTTGAGTCTGCAGCAAACCTTTCGGTGGAGACCTTGGAGAAGGGTTTACTCACTCCCAAGAGAAATGTATGGAGCTTTGGAGTCATGTTAC---------------
upper sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G068151_T01 (Zea mays), 3'ss of exon 4
ccaaacatcctaatattttgatgtgtttttactttacttg-tttgcattatatccat--agtggtcaatgccat--tgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
| | | || | | | | || || ||||| ||| | | | | || | | ||| |||| || ||| || || | | | || |||| |||||||| || ||||| ||||||||||| ||| |||| ||||||||||||||||| ||| |||||||||| || | |||||||||||||| |
---agttaacaagaatatatgtataatattgtgatataaaacctgcatcatacctgttaattaatcgacgtcatgttgttcactaaagat-ctgttttct-tcagTCTGCAGCAAACCTTTCGGTGGAGACCTTGGAGAAGGGTTTACTCACTCCCAAGAGCAACGTCTGGAGCTTTGGAGTCGTGTTACTGGAGCTAATAACTG
upper sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G828466_T01 (Zea mays), 3'ss of exon 2
---------------ccaaacatcct-aatattttgatgtgtttttactttacttgtttgcattatatccat--agtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAA-AGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
|| | | ||||| | || || | | || |||| ||| | | | | || | | ||| | | | | || | | || | || |||| |||||||| || ||||| ||||||||||| ||| |||| ||||||||||| || |||||| |||||||||| |
ataagtaacattgggtcagttaacaagaatatatgtataatattgtgatataaa-acctgcaccatacctgttaattaatcgacgtcatgttgttcactagAGATTTGTTTTCTTCAGTCTGCAGCAAACCTTTCGGTGGAGACCTTGGAGAACGGGTTTACTCACTCCCAAGAGAAATGTATGGAGCTTTGGAGTCATGT------------------
upper sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G010453_T01 (Zea mays), 3'ss of exon 2
ccaaacatcctaatattttgatgtgtttttactttacttg-tttgcattatatccat--agtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
| | | || | | | | || || |||| ||| | | | | || | | ||| | | | | || | | || | || |||| ||||||| || ||||| ||||||||||| ||| |||| ||||||||||| || |||||| |||||||||| | | |||||||||||||| |
---agttaacaagaatatatgtataatattgtgatataaaacctgcaccatacctgttaattaatcgacgtcatgttgttcactagagatttgttttcttcagTCTGCATCAAACCTTTCGGTGGAGACCTTGGAGAAGGGTTTACTCACTCCCAAGAGAAATGTATGGAGCTTTGGAGTCATGTTACTGGAGCTAATAACTG
upper sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G44630.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------ccaaacatcctaatattttgatgt--gtttttactttacttgtttgcattatatccatagtggtcaatgccatt--gtttaccgtggatgctattctttgtt----agGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG-
|||| || ||||| | | | | ||| || | ||| ||| ||| | | | | ||||| || || || |||| ||| |||||| || |||||| ||| ||||||| |||||||||| | || ||||| ||||||||||||||| | |||||| || | || ||||||||| | || |
taagttctctaactgataagtgttttatgttatgttattcaatatatccagttagagtctattatattcagccaatattctctatattcttttcttcatatttgtcataaatatttatatttattcctttatatttgttcccattcagtatattcatgaatttatttggtgtcgtccaggCTGTTGGAAACCTATCAATGGAAACACTGGAGAAAGGAATGCTCACTCCAAAGAGCAACGTATGGAGTTTTGGAATTTTTCTTCTGGAGCTACTTACTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatatccatagtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
ctattcttt CT-rich tract
attgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaaacatcctaatattttgatgtgtttttactttacttgtttgcattatatccatagtggtcaatgccattgtttaccgtggatgctattctttgttagGCTGCTGCAAACCTCTCAGTGGAAACCTTGGAGAAAGGTGTACTGACTCCCAAGAGCAACGTATGGTGCTTTGGAGTTGTCCTGCTGGAGCTAATAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
ccaaaca
- - - - - - - - -ttgatgt
- - - - - - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatgc