Sequence
atgc intronic sequence ATGC exonic sequencegtttatttaacaacttatcttgttgaaatctcatgattctcattgtaataattggtccctactactattgctcacatagacttttcaatttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0040g02090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 4
-----------------------gtttatttaacaacttatcttgttgaaatctcatg-attctcattgtaataattg---gtccctactactattgctcacatagacttttcaat---------ttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
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gtaaagcgtatctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT
upper sequence: Vv08s0040g02090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g10180.2 (Oryza sativa), 3'ss of exon 5
-----------------------gtttatttaacaacttatcttgttgaaatctcatg-attctcattgtaataattg---gtccctactactattgctcacatagacttttcaat---------ttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
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gtaaagcgtgtctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTGTGAAGAAGACTAAGAGT
upper sequence: Vv08s0040g02090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G36460.1 (Glycine max), 3'ss of exon 4
gtttatttaacaacttatcttgttgaaatctcatgattctcattgtaataattggtccctactactattgctcacatagacttttcaatttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
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------------gtttgtcttgtggaaatgatattcaaatccttctttt--tttatatacaat-ctatcttatatgcgaacatatatattcagGCATTTTCAGAAAGGTCTCCGCCTAGATCCAGAGCATAGTGAACTGAAAAAGGCATATTTTGGATTGAAAAATCTACTAAAAAAGAGTAAAAGT
upper sequence: Vv08s0040g02090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G03160.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttatttaacaacttatcttgttgaaatctcatgattctcattgtaataatt---ggtccctactactattgctcacatagacttttcaatttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
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-----------gtttggtctaacttcaaccttatt-ttcaatcagagagagtttggggtccaaaacagatatacttaagtaaactttctgtttcagGCATTACCAAAAAGGGCTTCGTCTTGATCCGGAACACAGTGAACTGAAGAAAGCATACTTCGGATTGAAAAAACTGCTCAAGAAAACAAAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcattgtaataattggtccctactactattgctcacatagacttttcaatttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
tgctcac putative branch site (score: 2)
cttttc putative PPT
ttttcaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttatttaacaacttatcttgttgaaatctcatgattctcattgtaataattggtccctactactattgctcacatagacttttcaatttagGCATTATCAAAAAGGTCTCCGTCTAGACCCAGAACATGGTGAACTGAAGAAAGCGTATTTTGGTTTGAAAAATTTACTGAAGAAAACTAAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA