Sequence
atgc intronic sequence ATGC exonic sequencegtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g06060.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT-
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--------------ctttttgttt-tgaattaaaagagtact-catcatacattggtt------------tatataacca-aagatatttatactgtctcaca-gtgactgataagatacattttccagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaa---taactgtaagttttctctccattctaacacatcccctt-cttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT
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------------------------------tgcatggatttcatgtggtct-ccaaggc--ttcaggcactgtagcataattcttatattttctttcttgcagccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT
upper sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 3
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT
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-------------------aattactgagctaaaagaccagctt-tgggcaaccgattc---tttatcatta-----ctgtgctttgggttgaaattgtacaagagattgatcttctaggattt-gcagTACTTTCTGTATCAGCTGTTGCGAGGATTAAAATATGTACACTCTGCAAATGTCTTGCACCGTGATCTAAAGCCCAGCAATTTGCTTCTGAATGCAAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT
ttctaac putative branch site (score: 1)
ttttctctccattcta CT-rich tract
ttctttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctcactctattcttgtttgtttctgtattaaaccatctcttcgttatccatcaattcaattcaagcactaaataactgtaagttttctctccattctaacacatccccttcttttttttttttgcagTATTTTCTCTATCAGGTACTACGAGGATTGAAGTATGTGCATTCAGCAAATGTCTTGCACAGAGACCTCAGGCCAAGTAATTTGCTGCTGAATGCGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT