Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatatccatttagtttttccttctcactttaaaagcaaaattcatggttccatccaccattccttattgctaatccacattattttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g53195.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G000052_T01 (Zea mays), 3'ss of exon 9
gtatgcatatccatttagtttttccttctcactttaaaagcaaaattcatggttcca--tccaccattccttatt-gctaatccacattattttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
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gtacgcatatctatc---cttttcttgttaatttggtaatcactagttgtggtttcacttccaccagccattcctagatcactgatcctgttctttgttcttcagGGTTGTGGAAATTGTTCGCCATAGGAACAGGGTAGAGGTTACCGTAAGCAGCGGCCAAACGTTTGTTGCGGATGCTGCTGTGGTCACTGTTCCGTTGGGT
upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 9
gtatgcatatccatttagtttttccttctcactttaaaagcaaaattcatggttccatccaccattccttattgctaatcca--cattattttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
||||||||| | |||| || ||| ||| | | | | | | | | || || | || | | || | || || | | ||||| |||||| | || |||||||||||| |||| ||||| |||||||||||||||||||| ||||||| |||||||| |||||||| | |||| || || |||
gtatgcataatatatc--ctttttattatcaatttgatatttagttgtagtttcactttcatcagccattgctccagcaccgacccttgttctttgttcttcagGGTTTTGGAAATTGTTCGCCACCGGAACAGGGTAGAGGTTACTGTAAGCAGTGGCCAAACATTCGTTGCGGACGCTGCAGTGGTCACTGTTCCGTTGGGT
upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G59050.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgcatatccatttagtttttccttctcactttaaaagcaaaattcatggttccatccaccattccttattgctaatccacatt--attttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
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---------------------gtacgattcatttgtcgaaggagtttc----caccatttaacgagtctgcagctaaaaccttattggacttttgttttgtcagAATTACCAAGATTTCAAGGCGCTACAGTGGTGTGAAGGTGACTACAGAGAAAGGAGACACGTTTGTTGCGGATGCTGCAGTCATTGCTCTTCCTCTAGGA
upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcatatccatttagtttttccttctcactttaaaagcaaaattcatggt-tccatccaccattccttattgctaatccacattattttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
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-------------gtaagcttttgcgttt---ttcaagag------ttatggcattcgtttagtgtttcacagtcataacct-cgtgtttctccttctctcagGGTTACTAAGATTGTCAGGCGGTACAATGGAGTGAAGGTAACGACAGAAAACGGGCAAACTTTTGTTGCGGATGCTGCAGTCATTGCTGTCCCTCTTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catggttccatccaccattccttattgctaatccacattattttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
tgctaat putative branch site (score: 2)
tccacattattttctt CT-rich tract
attattttcttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatatccatttagtttttccttctcactttaaaagcaaaattcatggttccatccaccattccttattgctaatccacattattttcttttctttagGGTTGTTGAGATTGTTCGCCACAGGAATAGGGTGGAGGTTACTGTAAGCAGTGGTAAAACATTTGTTGCGGATGCTGCAGTCATTGCTGTCCCCTTAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG