Sequence
atgc intronic sequence ATGC exonic sequence...ttgccggacgacatacgaaattccgccgcttttgacgcggagaaacgtaccgatcgatcgcgagctgattggtaatatggtatggattggatgggtgcagGTCGGCGGCGAAGGGAGGGAAGGCGGGGAAGGGGGAGAAGCGGGCGAGGCAGCCGCGGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g47560.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g47560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G812272_T02 (Zea mays), 3'ss of exon 1
-------ttgccggacgacatacgaaattccgccgcttttgacgcggagaaacgtaccgatcgatcgcgagctgattggtaatatggtatggattggatgggtgcagGTCGGCGGCGAAGGGAGGGAAGGCGGGGAAGGGGGAGAAGCGGGCGAGGCAGCCGCGGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGAC---
|||||| | | | | | | ||| | || | |||||| ||| | | | | ||| || |||||||| |||||| | || ||| || ||||| ||||||||| | ||||||||||| |||||||||||||||||||||||||||||||||||||||||
gcagcacttgccgcggacccggctagctggtggacgtacgcacgggaggagctgatgagatcgacgccga------cgccgacgccggctctcttgcttgt-tgcagGTCAGCGGCGGGGAAGGGCAAG---GGCAAGGGCGAGAAGCGGCAGCGGCAGCCGCGGATCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGACGGC
upper sequence: LOC_Os01g47560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G151763_T01 (Zea mays), 3'ss of exon 1
ttgccggacgacatacgaaattccgccgcttttgacgcggagaaacgtaccgatcgatcgcgagctgattggtaatatg-gtatggattgga---tgggtgcagGTCGGCGGCGAAGGGAGGGAAGGCGGGGAAGGGGGAGAAGCGGGCGAGGCAGCCGCGGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGAC
||| || | || ||| | ||| || | || || | |||||||| | ||| | | | | | | |||||||| |||||| || | ||| ||||| ||||||||| | |||||||||||||||||||| ||||||||||||||||||||||||| ||||||
-cgcctcac--tttccgctgacccggctagcttgctgctggtggggacgtcgtacgggag-gagctgatgagatcgatgcgcacgacgccggctcttgttgcagGTCAGCGGCGGCAGGCAAGGGCAAGGGCAAGGGCGAGAAGCGGCAGCGGCAGCCGCGGTTCGCGTTCTTGACCAAGAGCGAGGTCGACCACCTTGAGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtaccgatcgatcgcgagctgattggtaatatggtatggattggatgggtgcagGTCGGCGGCGAAGGGAGGGAAGGCGGGGAAGGGGGAGAAGCGGGCGAGGCAGCCGCGGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGAC
agctgat putative branch site (score: 4)
taatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgccggacgacatacgaaattccgccgcttttgacgcggagaaacgtaccgatcgatcgcgagctgattggtaatatggtatggattggatgggtgcagGTCGGCGGCGAAGGGAGGGAAGGCGGGGAAGGGGGAGAAGCGGGCGAGGCAGCCGCGGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGAC
- - - - - - - - - - - - gccgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtatg