Sequence
atgc intronic sequence ATGC exonic sequencegttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaataataataataataattccatgtttcttttttcttaattagtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os12g42300.1 (Oryza sativa), 3'ss of exon 11
gttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaataataataataataattccatgtttcttttttcttaattagtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
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------------------------------------gtcagtgattatacactccttatttttgtt-------------tctttcctgctttatcatgtacttttcggatttcatcagctatcgttgctgaaacagGCTTGGTGTCCTACCACTTGAGTTGAATAAACTGCTCATCATTGTTGTTGTACTGTCTATGGCGCTAACTCCATTACTCAATGAAATTGGAAGAAGGGCA
upper sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G06890.3 (Glycine max), 3'ss of exon 12
gttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaataataataataataattccatgtttcttttttcttaattagtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
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------------------------------------gtaagtaatta------tccaatatgatgcattggtgttatttgagttagaaaattgggattgtttttagttataaaatttgtggc-ttcttgtaagcagGCTTGGGGTGCTTCCCCTTGAGCTCAACAAGCTGCTCATAATTGTTGTTGTATTGTCAATGGCATTAACCCCATTTCTGAATGAAGCTGGAAGAAGGGCT
upper sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G30360.2 (Glycine max), 3'ss of exon 13
gttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaataataataataataattccatgtttcttttttcttaattagtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
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------------------------------------gtaagtaatta------tctaatgtgatgcattggtgctatttgaattagaaaattgggattgtttttagttataaaaatttgtggcttcttgtaagcagGCTTGGGGTGCTTCCTCTTGAGCTCAACAAGCTGCTCATAATTGTGGTTGTATTGTCAATGGCATTAACCCCATTTCTGAATGAAGCTGGAAGAAGGGCT
upper sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 12
gttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaat-aataataataataattccatgtttcttttttcttaatta-gtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
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---------------------------gtttttccaactgccaatattattgctcaaacatctcctcattatttcattagtttcgacattttcct--tactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataataattccatgtttcttttttcttaattagtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
tcttaat putative branch site (score: 3)
tttgtttccttcttgt putative PPT
tttcttttttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaataataataataataattccatgtttcttttttcttaattagtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT