Sequence
atgc intronic sequence ATGC exonic sequencegtattaacccgaagaaactacaaccttatttcagaacttaccccattttaatctaaaaattattgctgctgctaatatgtctccattttgaattgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os11g06420.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g06420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 4
--------gtattaacccgaagaaactacaaccttatttcagaacttaccccattttaatctaaaaattattgctgctgctaatatgtctccattttgaattgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC
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gtactgctgcactggcttcaatgaacattgttttattttcagaattgacagtattttaatctgacatatgttgttgcc---------------ttttggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATACAATGGAACTAGTCAAACAGTGGCAGGGAAAACAAGTCAGAGATTCTAC
upper sequence: LOC_Os11g06420.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
gtattaacccgaagaaactacaaccttatttcagaacttaccccattttaatctaaaaattattgctgctgctaatatgtctccattttga-----attgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC
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-tatt--tcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattttaatctaaaaattattgctgctgctaatatgtctccattttgaattgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC
tgctaat putative branch site (score: 2)
tctccatttt putative PPT
taatctaaaaattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaacccgaagaaactacaaccttatttcagaacttaccccattttaatctaaaaattattgctgctgctaatatgtctccattttgaattgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA