Sequence
atgc intronic sequence ATGC exonic sequence...atagatgagctcttaggttaccaactttcatgttatatggtttctgtatgacaataccttaaggacgctgcctaatttattttgtttctttctgtctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
Basic information
species | Oryza sativa |
transcript | LOC_Os09g12660.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 2
atagatgagctcttaggttaccaactttcatgttatatggtttctgtatgacaatacct-------taaggacgctgcctaatttattttgtttctttctgt-ctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
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--------tttccttcgctaaccacttacatgctgtcttccttctgtcctaaatttcccatctcacttattaccctggtttgttgatctgttttgcttccattctcagGGTACTGCAGATGCCGTGCGTCAATATATGTGGCTATTTGAGGAGCATAATATCATGGAGTTCCTTATTCTGGCTGGAGATCATCTGTACCGTATGGATT
upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 2
---atagatgagct-cttaggttaccaactttcatgttatatggtttctg-tatgacaataccttaaggacgctgcctaatttattttgtttctttctgtctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
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gtaatgccagcactgccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatc--attgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAATGTTTTGGAATTCTTGGTTCTGGCTGGTGACCATTTGTATCGAATGGATT
upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------atagatgagctctta--ggttaccaactttcatgttatatggtttctgtatgacaataccttaaggacgc-----tgcctaatttattttgtttctttctgtctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
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gtgcagattatttcttagcgtgtgagttgttgatttacactcaaagaaattggtgtttgcggtgcctggaacttgcattcgtaacgcgtaataactggc-cagaacacgttctgtaattga-aattcagtgatgatgtgattatgctcacaatgttgtaaactgttgtgattcagGGAACTGCTGATGCAGTCAGGCAATACCTCTGGCTCTTTGAAGAAGCTCAGGTTCTGGAGTACGTGATTTTAGCCGGAGATCACCTGTACCGTATGGACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgacaataccttaaggacgctgcctaatttattttgtttctttctgtctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
gcctaat putative branch site (score: 3)
tttattttgtttcttt CT-rich tract
taatttattttgtttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagatgagctcttaggttaccaactttcatgttatatggtttctgtatgacaataccttaaggacgctgcctaatttattttgtttctttctgtctcagGGTACTGCAGATGCTGTGCGACAATACTTATGGCTATTTGAGGAACACAATGTTATGGAGTTTCTCATTTTGGCTGGAGATCACCTGTACCGTATGGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgctgcc