Sequence
atgc intronic sequence ATGC exonic sequencegtatattgcttcgttttcattactttatcttcactaccttcttaattatgatggggtcaaacctagcagttgctatctgttacaatttcatatttatttgcgtcataacctttatcttatgattccaccctctattttagGTAGCATTTACGGGGAACTACAGTGAATACTTTGGATTTGCCACTGATGCTGATGCAGTAGTTTACTTGATGCTGGTAAATGATTTAATTCATGGACTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32660.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 13
gtatatt--gcttcgttttcattactttatcttcactacctt--cttaattatgatg--gggtcaaacctagcagttgctatctgttacaatttcatatttatt-tgcgtcataaccttt---atcttatgattccaccctctattttagGTAGCATTTACGGGGAACTACAGTGAATACTTTGGATTTGCCACTGATGCTGATGCAGTAGTTTACTTGATGCTGGTAAATGATTTAATTCATGGACTTT
||| || |||| | ||| |||||||||||| || | | | || || | | ||| | | | | | |||| | | |||||||| || | |||| | | | | || | | | || |||||||| ||||||||||||||| || ||| || ||||| |||||||| |||| |||||||| |||||||||||||||||||||||| |||||||||||||||
gtaatttaagctttatgcctgttagtttatcttcacttgctaagtctgactggaatactggattatgcctgggaactagt-tttgtt-tagtatcatatttgttatatatcattccttcttctaatctaaagtcatgcattttactttagGTAACATTTACGGGGAACTTCAATGAGTATTTTGGCTTTGCCACCGATGTAGATGCAGTGGTTTACTTGATGCTGGTAAATGATCTAATTCATGGACTTT
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 13
gtatattgcttcgttttcattactttatcttcactaccttcttaattatgatggggtcaaacctagcagttgctatctgttacaatttcatatttatttgcgtcataacctttatcttatgattccaccctctattttagGTAGCATTTACGGGGAACTACAGTGAATACTTTGGATTTGCCACTGATGCTGATGCAGTAGTTTACTTGATGCTGGTAAATGATTTAATTCATGGACTTT
|||| | | | | | ||| | || ||| | | | | | || ||| | || | | ||||||||||||| || || |||| ||| || ||||| ||||| ||||||| |||||| || |||||| |||||||| |||||| | |||||||| || |
----------------------------------------agcgattagccctgcaaagagtgcaaaggattatatttcactcatattctttctcaatcatttaattttttttcttttgcattattgaatctcgctgcagGTAGCATTTACTGGAAATTACAATGAGTATTTTGGTTTTGCAACTGATGTTGATGCTGTGGTTTACCTGATGCTGACTAATGATGTCATTCATGGGCTCT
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 13
gtatattgcttcgttttcattactttatcttcactaccttcttaattatgatgggg--tcaaacctagcagttgc-tatctgttacaatttcatatttatttgcgtcataacctttatcttatgattccaccctctattttagGTAGCATTTACGGGGAACTACAGTGAATACTTTGGATTTGCCACTGATGCTGATGCAGTAGTTTACTTGATGCTGGTAAATGATTTAATTCATGGACTTT
|| |||| | | || | | || | || ||| | ||| | | | | | || ||| | || | | | |||||||||||||| || || |||| ||| || ||||| ||||| ||||||| |||||| || ||||| |||||||| |||||| | |||||||| || |
------------------------------------------tagcagtgattagcctttgaatcgaaagattatatttcacttagatattctttctcaatcatttaatt-tttttcttttgcattattgaatgtgactgtagGTAGCATTTACTGGAAATTACAATGAGTATTTTGGTTTTGCAACTGATGTTGATGCTGTGATTTACCTGATGCTGACTAATGATGTCATTCATGGGCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatatttatttgcgtcataacctttatcttatgattccaccctctattttagGTAGCATTTACGGGGAACTACAGTGAATACTTTGGATTTGCCACTGATGCTGATGCAGTAGTTTACTTGATGCTGGTAAATGATTTAATTCATGGACTTT
tcataac putative branch site (score: 2)
ttccaccctctatttt putative PPT
tttatcttatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattgcttcgttttcattactttatcttcactaccttcttaattatgatggggtcaaacctagcagttgctatctgttacaatttcatatttatttgcgtcataacctttatcttatgattccaccctctattttagGTAGCATTTACGGGGAACTACAGTGAATACTTTGGATTTGCCACTGATGCTGATGCAGTAGTTTACTTGATGCTGGTAAATGATTTAATTCATGGACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA