Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttatgaatcatacatcattttttgttcaccttttctgatgttttacagcagcaggggcacttctaacgtctttcaaaccttctcccagGTACCTGCATGAGGTGTGCTTGCCATCTGTTGTGCATAGAAACTTTAAGTCCTCAAACATCCTACTCGATGAAGAGCATAATCCACATTTATCTGACTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g09740.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 12
gtaagttttatgaatcatacatcattttttgttcaccttttctgatgttttacagcagcaggggcacttctaacgtctttcaaaccttctcccagGTACCTGCATGAGGTGTGCTTGCCATCTGTTGTGCATAGAAACTTTAAGTCCTCAAACATCCTACTCGATGAAGAGCATAATCCACATTTATCTGACTGT
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gtaagttt---ggaccgtactgcatttttactcca--------aaggtt--atggcag--aggatgcatataatgtcttccaagttttcttgtagGTACCTGCATGAGGTGTGCATGCCGTCTCTTGTTCATAGAAATTTGAAGTCTTCAAACATTCTACTAGATGAGGAGCATAATCCACACCTATCTGACTGT
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA09G00970.1 (Glycine max), 3'ss of exon 12
------------------------------------------gtaagttttatgaatcatacatcattttttgttcaccttt---tctgatgttttacagcagcaggggcacttctaacgtctt---tcaaaccttctcc--cagGTACCTGCATGAGGTGTGCTTGCCATCTGTTGTGCATAGAAACTTTAAGTCCTCAAACATCCTACTCGATGAAGAGCATAATCCACATTTATCTGACTGT
| || | | | | | || || | | || ||| | || || |||| |||| | | | || | ||||||||||||||| ||||||||||| |||||||| |||||||| || || || |||| || |||| ||||| |||| ||||| || | |||||||||
gtatgtttcattcacatctgacatattaagtctctctttggcatggccttgactggctacccgacccccctgtttttccctcaagtagagtgagttagcatatcacattcagg-ctaatttcttgagttatgctttgtatgtcagGTACCTGCATGAAGTGTGCTTGCCTTCTGTTGTACATAGAAATTTCAAATCTGCAAATATATTACTTGATGAGGAGCTCAATCCTCACCTGTCTGACTGT
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G11820.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------------gtaagttttatgaatcatacatcatttttt---gttcaccttttctgatgttttacagc-----agcaggg-gcactt---ctaacgtctt---tcaaaccttctcc--cagGTACCTGCATGAGGTGTGCTTGCCATCTGTTGTGCATAGAAACTTTAAGTCCTCAAACATCCTACTCGATGAAGAGCATAATCCACATTTATCTGACTGT
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gtatgttacattcacatatctgacatattaagtctctccttggcatggccttgactggctactccacccccctgcttttccctcaagtatatttgttttagccttgtagagtgagttagcatgtcacattcaggctaatttctcaagttatgctttgtctatcagGTACCTGCATGAAGTGTGCTTGCCTTCTGTTGTACATAGAAATTTCAAATCTGCAAATATATTACTCGATGAGGAGCTCAATCCTCACCTGTCTGACTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgatgttttacagcagcaggggcacttctaacgtctttcaaaccttctcccagGTACCTGCATGAGGTGTGCTTGCCATCTGTTGTGCATAGAAACTTTAAGTCCTCAAACATCCTACTCGATGAAGAGCATAATCCACATTTATCTGACTGT
ttctaac putative branch site (score: 1)
ccttctccc putative PPT
tgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttatgaatcatacatcattttttgttcaccttttctgatgttttacagcagcaggggcacttctaacgtctttcaaaccttctcccagGTACCTGCATGAGGTGTGCTTGCCATCTGTTGTGCATAGAAACTTTAAGTCCTCAAACATCCTACTCGATGAAGAGCATAATCCACATTTATCTGACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA