Sequence
atgc intronic sequence ATGC exonic sequencegtattctttcttatcactgctctctgactagaaatggctggtactggttcctattgtcttgatgttttatcctgcactggcagATCCAGGCACAAATCGTATGAATGAAGCAGATCAACAAGCACCTGCAAAGCTGAAATTGCAGTTATTTCCAATCAATGAAGCCACACGAAAGGCATTGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g56234.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 8
----------------------------------------gtattctttcttatcactgctctctgactagaaatggctggtactggttcctattgtcttgatgtttt-atcctgcactggcagATCCAGGCACAAATCGTATGAATGAAGCAGATCAACAAGCACCTGCAAAGCTGAAATTGCAGTTATTTCCAATCAATGAAGCCACACGAAAGGCATTGGA
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gtatggcttgtagcaactggattttagttcttgtagttgttgaactttgttcaacac-acattgaaattaacagtagcagatacaggt--ctactgtcatgatgtttttgttctgcatttgcagGCATTAGCACAAATCATATGAAGGAAACAGATTCACAAGCACCTGTGAAGCTGAAGCTACAGTTATTTCCAATAAACGAAGCTACTCGAAAGGCATTGGA
upper sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 8
----------------------------------------gtattctttcttatcactgctctctga-ctagaaatggctggtactggttcctattgtcttgatgtttt-atcctgcactggcagATCCAGGCACAAATCGTATGAATGAAGCAGATCAACAAGCACCTGCAAAGCTGAAATTGCAGTTATTTCCAATCAATGAAGCCACACGAAAGGCATTGGA
| | || | | ||| | | | || | | || ||| ||| ||||| || ||||||||| || ||||||| |||| ||||||||| |||||| ||||||||| ||| ||||||| |||||||| | |||||||||||||| |||||||| || || |||||||||||
gtatggcttctagcaactggattttagtttttgtatttgtggaactttgttcaacacagtcgttgaagttaacagtagcaaatacaggt--ctattatcctgatgtttttattctgcacttgcagGCATTAGCACAAATCATATGAAGGAAGCAGATTCACAGGCACCTGTGAAGCTGAAGCTACAGTTATTTCCAATAAATGAAGCTACTCGGAAGGCATTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaaatggctggtactggttcctattgtcttgatgttttatcctgcactggcagATCCAGGCACAAATCGTATGAATGAAGCAGATCAACAAGCACCTGCAAAGCTGAAATTGCAGTTATTTCCAATCAATGAAGCCACACGAAAGGCATTGGA
tcttgat putative branch site (score: 4)
atgttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattctttcttatcactgctctctgactagaaatggctggtactggttcctattgtcttgatgttttatcctgcactggcagATCCAGGCACAAATCGTATGAATGAAGCAGATCAACAAGCACCTGCAAAGCTGAAATTGCAGTTATTTCCAATCAATGAAGCCACACGAAAGGCATTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC