Sequence
atgc intronic sequence ATGC exonic sequencegtaagatcatttcggtagagttgttatgaacaaaatattctggcgtattgttctaacttctttgtcatgtgttatgttcagaagCACCCTGCAGTCACCCCTGCCAGCTTCCCGCAAATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44944.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44944.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100246_T01 (Zea mays), 3'ss of exon 3
------------------gtaagatcatttcggtagagttgttatgaacaa-aatattctggcgtattgttctaacttctttgtcatgtgttatgttcagaagCACCCTGCAGTCACCCCTGCCAGCTTCCCGCAAATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGG
|| || | | || || || | || |||| | | ||||||| | || || | | || ||||| |||||||||||| |||||||| |||| ||| ||| |||||||| | | ||||| ||||| |||||||||||||||| ||| |||| ||||| |||
aatgtatctagaaataccaaaatgtcttataatatgaaatggagggagtactaagtttctagtgctttgttcttattttcttacccaccttcattttcagCGGCACCCTGCAGTTACCCCTGCTAGCTACCCCCAAGTTCAGGCATCAATTGTATCGAATCCCACCTTTTGGGAAAGAATTGGTAGCGACACATTAGCTA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaaatattctggcgtattgttctaacttctttgtcatgtgttatgttcagaagCACCCTGCAGTCACCCCTGCCAGCTTCCCGCAAATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGG
ttctaac putative branch site (score: 1)
atattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatcatttcggtagagttgttatgaacaaaatattctggcgtattgttctaacttctttgtcatgtgttatgttcagaagCACCCTGCAGTCACCCCTGCCAGCTTCCCGCAAATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA