Sequence
atgc intronic sequence ATGC exonic sequencegtttggattgttctcgtctctatagaacatgttactcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01240.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G467385_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------gtttggattgttctcgtctctatagaacatgtt-----actcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | || | ||| || |||| |||| | ||| |||||||| ||||||||||||| ||||||||| ||||| || |||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctgctaactttttttgtaaaatatttctccaaagattacaatctgattaaactagctcaaagaaaatccaattattaacttgggtgcatcatgagtcatgaccattggctgctctgcagATCCTTGAACCTTGCCAGTCAAGTATCGCATATCGATCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G419699_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------gtttggattgttctcgtctctatagaacatgtt-----actcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | || | ||| || |||| |||| | ||| |||||||| ||||||||||||| ||||||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctactaacttttttgtaaaatatttctccaaagattacaatctgattaaactagctcaaagaaaatccaattattaacttgggtgcatcatgagtcatgaccattggctgctctgcagATCCTTGAACCTTGCCAGTCAAGTATCGCATATCGACCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G435765_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------gtttggattgttctcgtctctatagaacatgtt-----actcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | || | ||| || |||| |||| | ||| ||||| || ||||||||||||| ||||||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctgctaacttttttgtacaatatttctccaaagattacaatctgattaaactagctcaaagaaaatccaattattaacttgggtgcatcatgagtcatgaccattggctgctctgcatATCCTTGAACCTTGCCAGTCAAGTATCGCATATCGACCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G481210_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------gtttggattgttctcgtctctatagaacatgtt-----actcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | || | ||| || |||| |||| | ||| |||||||| ||||||||||||| ||||||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctgctaacttttttgtaaaatatttctccaaagattacaatctgattaaactagctcaaagaaaatccaattattaacttgggtgcatcatgagtcatgaccattggctgctctgcagATCCTTGAACCTTGCCAGTCAAGTATCGCATATCGACCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G414487_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------gtttggattgttctcgtctctatagaacatg-----ttactcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | || ||||| || |||| |||| | ||| |||||||| ||||||||||||| ||||||||| ||| | || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctgctaactttttttgtaaaatatttctccaaagattacaatctgattaaactagctcaaagaaaatccaattatttacttgggtgcatcatgagtcatgaccattggctgctctgcagATCCTTGAACCTTGCCAGTCAAGTATTGCAAATCGACCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G457909_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------gtttggattgttctcgtctctatagaacatgtt-----actcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | | || | ||| || |||| |||| | ||| |||||||| ||||||||||||| ||||||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctgctaacttttttgtaaaatatttctccaaagattacaatctgattaaactagcttaaagaaaatccaattattaacttgggtgcatcatgagtcatgaccattggctgctctgcagATCCTTGAACCTTGCCAGTCAAGTATCGCATATCGACCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC
upper sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G179406_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------gtttggattgttctcgtctctatagaacatgtt-----actcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
| |||| || | | | || | ||| || |||| |||| | ||| |||||||| ||||||||||||| ||||||||| ||||| || ||||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||| |||||||
gtgtccattcctgctaactttttttgtaaaatatttctccaaagattacaatctgattaaactagctcaaagaaaatccaattattaacttgggtgcatcatgagtcatgaccattggctgctctgcagATCCTTGAACCTTGCCAGTCAAGTATCGCATATCGACCTCCAAATCCCTGGACCATGGGAATTCTAAGTCTACTTGCTGAAATTTATAATCTTCCAAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagaacatgttactcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
tcataac putative branch site (score: 2)
ttattatcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggattgttctcgtctctatagaacatgttactcaggcatgcttattatcataaccagtaattgcactgcagATTCTTGAACCTTGCCGGTCAAGTATAGCATACCGTCCTCCAAATCCCTGGACAATGGGGATTCTTAGTCTGCTTGCTGAGATCTATAATCTACCAAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC