Sequence
atgc intronic sequence ATGC exonic sequence...tatcaagcaattctacatcatggtattctgtgtctatgatcgatgaatccatgcatttaacatgcaatactttttgtttcattttctttcactcatctagAAAAGGACATGCATTTGGAGGAGGATGAACAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAATCGCCTCCTCGTGCTCGTGAAAATGGCAACGC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g08400.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 3
tatcaagcaattctacatcatggtattctgtgtctatgatcg----atgaatccatgcatttaacatgcaatactttttg-tttcattttctttcactcatctagAAAAGGACATGCATTTGGAGGAGGATGAACAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAATCGCCTCCTCGTGCTCGTGAAAATGGCAACGC
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-gttactcagtt-tacttcatg-tctttagtgctgttagttttcttatgaattcatgcagttaatgtgtgacactttctggtttaatttgtttttact--tctagATAAGGATATGCATTTGGAGGAGGATGAGCAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAGTCACCCCCTCGCAGAAATGGCAGTGCCAATGG
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 4
tatcaagcaattctacatcatg-gtattctgtgtctat--gatcgatgaatccatgcatttaacatgcaatactttttgtttcattttctttcactcatctagAAAAGGACATGCATTTGGAGGAGGATGAACAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAATCGCCTCCTCGTGCTCGTGAAAATGGCAACGC---
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--ataattatttttccattgaatgcatcttatttttatatgatcctatagagtaaatatttcttgtctcttagttttttttttttttctatttatctgt-tagATACTGAATCTCAATTGGAGGAAGATGAACAACTTGCTAGAGCTCTTCAAGAGAGTTTGAACGTGGAGTCTCCTCCTCGA---CATGATGCTGGAAATATATT
upper sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 3
-tatcaagcaattctacatcatggtattctgtgtctatgatcgatgaatccatgcatttaacatgcaatactttttgtttcattttctttcactcatctagAAAAGGACATGCATTTGGAGGAGGATGAACAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAATCGCCTCCTCGTGCTCGTGAAAATGGCAACGC---
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gctttacttatcaaaaaaaattattagcaaatatcttccattttttgattcttataatttgtct-tactacagttaataagtttctgaaatgattggatagATAATGAATTTCAATTGGAGGAAGATGAACAACTTGCTAGAGCTATACAAGAGAGCTTGAATATTGAGTCTCCTCCACAA---CATGGAAATGGAAATGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatccatgcatttaacatgcaatactttttgtttcattttctttcactcatctagAAAAGGACATGCATTTGGAGGAGGATGAACAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAATCGCCTCCTCGTGCTCGTGAAAATGGCAACGC
atttaac putative branch site (score: 3)
ctttttgtttcatttt putative PPT
tttttgtttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcaagcaattctacatcatggtattctgtgtctatgatcgatgaatccatgcatttaacatgcaatactttttgtttcattttctttcactcatctagAAAAGGACATGCATTTGGAGGAGGATGAACAACTTGCAAGAGCTATCCAGGAAAGTTTGAATGTTGAATCGCCTCCTCGTGCTCGTGAAAATGGCAACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC