Sequence
atgc intronic sequence ATGC exonic sequencegtttttattttcgggtctttcaggttttccctcctctttttggatttttaatatgtggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
----------gtttttattttcgggtctttcag-----gttttccctcctctttttgg--atttttaat--atgtggtgaa--atgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
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aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatccatttgacagttcatttttcctttatgcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG
upper sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G07110.1 (Glycine max), 3'ss of exon 2
------------------gtttttattttcgggtctttcaggttttccctcctc---tttttggatttttaatatgtggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
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attttacaaagctcatccaaacacacactaagtaatgtctgttcttatttatataaatatttggagttccctaatgtagttttagtttcatttgtttcagATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTACTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAA
upper sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G23610.1 (Glycine max), 3'ss of exon 2
------------gtttttattttcgggtc----tttcaggttttccctcctctttttggatttttaatatg-----tggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
|||| || | | | | | | | | | || | || | ||| | || | | | ||| || || ||||||||||| ||||| ||||||||||||||||||||| ||||||||| | |||| |||| || | | |||||| ||||||||||||||
atcactctttttcttttccttgttgaataactatatgatgatatatctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
upper sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G07750.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------gtttttattttcgggtctttcaggttttccctcctctttttggatttttaatatgtggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
|| ||| | || | || | | ||| | ||| | || | | || | || | ||||||||||| ||||| || || ||||||||||||||||| |||||| | || | || | | ||| || ||||||| |||| | |||
gtgggacttgaatttttcaaatggctagcaaaataatacaacacgagtcaccaatgtactgccaacaaatatcaaaatcaactttgtctttgtgcaaaatcattagatattcacgttatctagtttagctttatgatctcttgt----tattattgcattgcagATGATTCCTGTAGCCGCTAATGATGTTGCTTTCTCCATTCATTCAGTCATATTAAATTTAATTATACTGTCCCAAATTTCAATGTTTGAA
upper sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
-------gtttttattttcgg----------gtctttcaggttttccctcctctttttggatttttaatatg----tggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
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ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccctcctctttttggatttttaatatgtggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
ttttaat putative branch site (score: 3)
ttttcttgtt putative PPT
tttttggatttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttattttcgggtctttcaggttttccctcctctttttggatttttaatatgtggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT