Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctcatatggtgcattgatattacagacaagtttttcagtgctcttctgaaatcctaatagcatatgagctggtttttctgttgagttgccatttttattcgggagaaatctcttcatttggctgtttctttcctgcagAAAGATTGTTTCGAAATCTATGCTCTGGTTCCTGGACTTCTACGCGAAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g48370.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g48370.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G421899_T03 (Zea mays), 3'ss of exon 8
---------------------gtaagtctcatatggtgcattgatattacagacaagtttt--tcagtgctctt-ctgaaatcctaatagcatatgagctggtttttctgttgagttgccatttttattcgggagaaatctcttcatttggctgtttctttcctgcagAAAGATTGTTTCGAAATCTATGCTCTGGTTCCTGGACTTCTACGCGAAGAG
| |||||| ||||| ||||| | ||||| | | || | | | | | || || | ||| ||| ||| | ||| | || | || | | ||||||| | || ||| ||||||||||||||| || ||| ||||||| || ||||||||||||||||| || |||
gtaagttcagcctgtattgttttgttaatcatattgtgcag-agtattatgtgtatgttttgattatagcctgtaccatgaattgatttttttacaaggcagctttgctggtgaacttccactgaattttgaactaagttacaccatttggttattgcttccctgcagAAAGATTGCTTTGAAGTCTATGCACTAGTTCCTGGACTTCTACGTGAGGAG
upper sequence: LOC_Os02g48370.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G110109_T01 (Zea mays), 3'ss of exon 9
gtaagtctcatatggtgcattgatattacagacaagtttttcagtgctcttctgaaatcctaatagcat-----atgagctggtttttctgttgagttgcc----------atttttattcggga--gaaatctcttcatttggctgtttctttcctgcagAAAGATTGTTTCGAAATCTATGCTCTGGTTCCTGGACTTCTACGCGAAGAG
|||||| | || |||| | | || || ||| | ||| | || || | | ||||| | |||| |||||||| | || || | || | | | ||| | | |||||| | || ||||||||||||||||||| || ||| | ||||| || ||||| ||||||||| | || |||
gtaagttcagtt---tgtattgttttgttagtcatgttgtgcag-attattatgttttgattatagcctgtaccatgaaatggtttttttacaaggtagctttgctagggaacttccactgagatttgaagttacactatttggttattgctttcctgcagAAAGATTGCTTTGAAGTTTATGCACTAGTTCCGGGACTTCTAAGAGAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgccatttttattcgggagaaatctcttcatttggctgtttctttcctgcagAAAGATTGTTTCGAAATCTATGCTCTGGTTCCTGGACTTCTACGCGAAGAG
ctgtttctttcctgc CT-rich tract
atttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctcatatggtgcattgatattacagacaagtttttcagtgctcttctgaaatcctaatagcatatgagctggtttttctgttgagttgccatttttattcgggagaaatctcttcatttggctgtttctttcctgcagAAAGATTGTTTCGAAATCTATGCTCTGGTTCCTGGACTTCTACGCGAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA