Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataactcttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 5
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataactcttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
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------------------------------gtaaggtttatctgtactttacaccaacacaaatatatattttttagtattggttattgagggtac-cttgtcttgaactatc------agGCAAACTTCTCTGTTCCAGTTCTCTGCTTTGCTAGAAATGTTGCATGCAATGTCAGGGGTGGTTTTTTCAA
upper sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 4
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataactcttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
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----------------------------------------gtgatgttcatggcccgtataccaatacaaatata-tcatattgtcactaacaggatttctcctttccaccacct----agGCAAATTGTTCTATCCCAGTTCTGTGTGTAGCCAGAAACGTTGCATGCAATGTTAGGGGTGGTTTCTTCAA
upper sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G25010.1 (Glycine max), 3'ss of exon 4
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataact-cttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
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------gtaaattttctttcttgtatagttggaagcc-caatactttcaattggatgaatgc-------aattttgcccttttttcactaatatgaactgattaaatctgtttgtcttgtagGCAAGCAATACTATCCCTGTTCTGTGTGTTGCAAGAAATGTTGCTTGCAATGTTAGGGGTGGCTTCTTTAA
upper sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 4
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataact-cttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
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------gtaaattttctttcttgtatagttggaagcc-caattctttcaattgcacgaatg-------gaattttgtc--ttttttcactatatgaactgattaaacctgtttgtcttgtagGCAAGCAATACTATCCCTGTCCTATGTGTTGCAAGAAATGTTGCTTGCAATGTTAGGGGTGGCTTCTTTAA
upper sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 4
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataact-cttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
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------------------------gtaatttcacttacctatataatgtgatactaatatacat---aaaatttcattgtttctgtagtgttctgaactgattaaacttgtttatcttgtagGCAAGCAATGCAGTCCCTTTCTTGTGTCTTGCAAGAAATGTTGCTTGCAATGTTAGGGGTGGCTTCTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagatttaaccatttctttgatgatgtgcactcatcataactcttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
tcataac putative branch site (score: 2)
ctcttctttt CT-rich tract
atttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaccattgcacttggttatgcagttgaaagcttcaatactgttaaataataacatgctttttaagatttaaccatttctttgatgatgtgcactcatcataactcttcttttgaagGCAAATAATGCTATTTCCGTCCTGTGTGTTGCAAGAAATGTTGCATGCAATGTCAGAGGTGGTTTTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA