Sequence
atgc intronic sequence ATGC exonic sequencegtaatatgctaaattattagtgttttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 9
---------------------------------gtaat-atgctaaattattagtgt-tttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
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gtacaagctgttatgtgttttccattctgttgtgtatttgcgctaaactataaccttatttatgtttggccttgaagtttgttcattacaagtccctttttgctacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCC
upper sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G412899_T05 (Zea mays), 3'ss of exon 9
-------------------------gtaatatgc-taaattattagtgttttatccactatgtttattttgagttgatttatctgaatttatttc------acagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
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gtacaagctgttctatatcctttttgttgtgtttatggacttctaataacctgagttcagtctgtctgtgaagtttgttcattacaagttccttttttggtacagTTGTTTTTATTGGCACAACGCTCTTTGCTTTACAACAGTTATCCGGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCC
upper sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G21860.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------gtaatatgctaaattattagtgttttatccactatgt-------ttattttgagttgatttat--ctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
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gtacataactacatatcataatattttattcttttggaacagtagtgtatcttttagacgattgcttaatcatatcataattt-ctaattcatttgtttttgcaatagtatatagttgtcttatttatggttgctaaatcactaaatgcattttgcagTGATGTTCATTGGATCTACACTTTTTGCGTTGCAGCAGCTATCTGGCATAAATGCTGTTTTCTATTTCTCTTCAACTGTCTTTGAAAGTTTTGGTGTACC
upper sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G02200.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------gtaatatgctaaattattagtgttt-------tatcca-ctatgtttattttg-agttgatttatc--tgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
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gtacataactacatatcataatattttatttttttggaacagtagtgtatcttttagatgattgctcgatcatatcataatttctaaaatcatttgtttttgtaagagtatatagttgcgtcttttttatggttgctaaatcactaaatgcattttgcagTGATGTTCATTGGATCTACACTTTTTGCGCTGCAGCAGCTATCTGGCATAAATGCTGTTTTCTATTTCTCTTCAACTGTCTTTGAAAGTTTTGGTGTACC
upper sequence: Vv09s0002g04380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G79820.4 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------gtaatatgc---taaattattagtgttttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
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ccaaaaaaatgacattttcatttgccaaaaacatacatatagatgatgtgtagcctcttaattaccttcatttttac---gtttaaattttctccgattgcagTGGTTTTCATTGGATCTACCCTTTTTGCTTTACAACAGTTGTCTGGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgttttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
agttgat putative branch site (score: 5)
tttatttc putative PPT
ttgatttatctgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatgctaaattattagtgttttatccactatgtttattttgagttgatttatctgaatttatttcacagTGGTTTTCATTGGATCAAGCCTATTTGCTTTACAACAGCTTTCTGGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA