Sequence
atgc intronic sequence ATGC exonic sequencegtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaagttctttgtgttttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 4
gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaagttctttgtgttttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
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-------gtaagccatggctatctttctgcatgatcatgctggcactaatattg-----acaccatgtgagcatcatttc--ctcctgttgact-gttatgttcaatg---tgcagCAATTGGAGCCATCTTTTCTGCGACAGATTCTGTCTGCACATTGCAG
upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaa-gttctttgtgttttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
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gtgtgcttaaatt---accttcttttacagtaatttgttggacttaactccaaacttggaacattcccttctt------ccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
upper sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaagttctttgtgttttctcttattacaatttcatttcttgttctctca-tctcactcaatgattt-gcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
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--------------------------------gtaccctgaaacaaagaaaacccttttcaagt-tcttattc--attaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
atctcac putative branch site (score: 3)
ttattacaatttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaagttctttgtgttttctcttattacaatttcatttcttgttctctcatctcactcaatgatttgcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA