Sequence
atgc intronic sequence ATGC exonic sequencegtgaaacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 5
-------------------------gtga-aacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
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ttgtgagaaacatatggatgaaagcgtaatgagaatagttgtggtgtggaaattttctatttattcatgctta--tcctttgaaatgatatttt--tcaatt-agCTGCTGGAGCTGGCTTGACGGGGAGCAAAATGGCCAGAAGAATTGGGAGCGTGAAAGAATTTGAGTTCAAACCTATTGGTGAAAACCATAATCAGGGT
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G05680.1 (Glycine max), 3'ss of exon 5
-gtgaaacaactgttacattttttgggcttcttgcttctggaatcctggtttctt--------------tctac-taatactttcatcaac-----ccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
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attgtgataaaagttgcatctgttggacaattgactccttgcatattccttttttaaattaagaaattttttatgtatctctttgttctacttttgccagCTGCTGGAGCTGGACTTACTGGAAGCAAAATGGCTAGGAGAGTTGGGGGTGTTGATGAGTTTGAATTCAAGGCTATAGGAGAAAACCATAACCAAGGC
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G24310.1 (Glycine max), 3'ss of exon 5
--------gtgaaacaactgttacattttttgggc--------ttcttgcttctggaatcctggtttctttctactaatactttcatcaac-----ccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
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ccttgatcttgcagttatttctactttttttttatatcagttattttccttttttaaatgatgaattttttcgtgtatctctttgttctacttctgccagCTGCTGGAGCTGGACTTACTGGAAGCAAAATGGCTAGGAGAGTTGGGGGTGTTGATGAGTTTGAATTCAAGGCTATAGGAGAAAACCATAACCAAGGC
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 5
---------------------gtgaaacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
| ||| | || | | | || || | || || || || || || | | ||||||||| ||||||||||| || || ||||||||||||||| ||| ||| || || ||||| ||||||||| | ||||||||||||||||||||
tcattcagttttgttttgttttttgtgtgtgtgtgttgctgttggtgatgctccatttttagatgatgaagatattttatgtatcactttgttttactagCTGCTGGAGCTGGACTCACTGGAAGCAAAATGGCTAGAAGAGTTGGGGATGTTGAGGAGTTTGAATTCAAAGCTGTAGGAGAAAACCATAACCAAGGT
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G17160.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------gtgaaacaactgttacatttttt---------gggcttcttgcttctggaatcctggtttctttctactaatactttcatcaac-----ccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAA--CTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
|| | | | ||| |||||| | || | || | ||| || | ||| || |||| || || ||||||||||| |||||| | || || || ||||||||||| ||| | | |||| ||||| ||||| ||||| ||||| |||||||||||||||||||||
gttcttatctgttattgtgataaaagttgcatctgttggacaattgccttcttgatcttgcagttatttctacttttttttttatatcagttattttccttttttaaatgatgaaattttttgtgtatctctttgttctacttctgccagctgctggagctggatttactggaagcaaaatggctagGAGAGAGTTAGGGGTGTTGATGAGTTTGAATTCAAGGCTATAGGAGAAAACCATAACCAAGGC
upper sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------gtgaaacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
| ||| | | | | | | | | | | | | ||| ||| ||||||| || ||||| || ||||||||| ||||| ||||| |||| || |||||||| |||||||| | || || ||||| |||||||||||||||||||| ||||| |||||
gtaaataaaaagtagaatcagttttagattcctttaagaaataaaatgaatcaaagtgatgataattgtatagttcttagtcttctgttttgtttctac--atgtgttcatgaat--agCTGCTGGAGCTGGGCTCACTGGGACGAAGATGGCTAGGAGAACTGGTGACATTGAAGAGTTTGAATTCAAAGCTATTGGAGAAAATCATAATCAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
tactaat putative branch site (score: 1)
ctttcatc CT-rich tract
taatacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaacaactgttacattttttgggcttcttgcttctggaatcctggtttctttctactaatactttcatcaacccagCTGCTGGTGCTGGACTCACAGGGAGTAAAATGGCTAGAAGAACTGGAAGTGTCGATGAATTTGAGTTCAAAGCTATTGGAGAAAACCATAACCAAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA