Sequence
atgc intronic sequence ATGC exonic sequencegtatatcaaagctcctgttatcaaccttgtttatgttcagcagatgcattcacatgcaccatattttatacaactatataatatgacatgcttattaaagacgtgaatatatgcaattttgtctttcttcatttgcttgatgaatgggttctgcttgagcttgtatacattatgatatgtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 3
gtatatcaaagctcctgttatcaaccttgtttatgttcagcagatgcattcacatgcaccatattttatacaactatataatatgacatgcttattaaagacgtgaatatatgcaattttgtctttcttcatttgcttgatgaatgggttctgcttgagcttgtatacattatgatatgtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
| | || | | | | ||||||| ||| |||||| || || |||| || | || ||| |||| | | | | |||| || ||||||||||| || ||||| || |||||||||||||||||||| ||||||||||| |||
----------------------------------------------------------------------------------gtatccacctccctcaccagttaaatatattttatt--gtcttttagtgttatttttttgaactagtagaacatgtgctaatatat-------tgtacttatgctttagAACGGCAAGCAAATGGTGCAAGAGGGAGCATTGACAGCTTTAGCATCAGTAGCTGATTCATCGCAG
upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 3
gtatatcaaagctcctgttatcaaccttgtttatgttcagcagatgcattcacatgcaccatattttatacaactatataatatgacatgcttattaaagacgtgaatatatgcaattttgtctttcttcatttgcttgatgaatgggttctgcttgagcttgtatacattatga-----tatgtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
|| | | | | | |||| || | |||||| | ||| | | | | ||| |||| | | ||| | || ||||||| ||||||||||| |||||||| || |||||||||||||| ||||| || ||||||||||||
----------------------------------------------------------------------------------------------gtatgcatttacttgtgttgaattaggtatca----gcttgctttaaaaatatttgttatcatggttagtaaacatgctaactgctcttgttcatattctagAATGGAAAGCAAATGGTGCAGGAGGGAGCATTGACAGCTTTAGCGTCAGTAGCAGATTCATCACAG
upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G29010.1 (Glycine max), 3'ss of exon 3
gtatatcaaagctcctgttatcaaccttgtttatgttcagcagatgcattcacatgcaccatattttatacaactatataatatgacatgcttattaaagacgtgaatatatgcaattttgtctttcttcatttgcttgatgaatgggttctgcttgagcttgtatacattatgatat-gtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
|| |||| | | | || || ||| | ||||| |||||| | | | | | | |||| || | | | | || |||||||||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| ||| ||
------------------------------------------------------------------------------------------aataataaatattttgacatgcatgcttcctattttatgcattt--ctgatgattagtgtttaaatatgtagttatattttcttttcttgcccatgttctagAATGGGAAGCAAATGGTTCAAGAAGGGGCTTTGACAGCCTTAGCATCTGTTGCAGATTCTTCAGAG
upper sequence: Vv08s0007g07240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G04400.2 (Glycine max), 3'ss of exon 3
gtatatcaaagctcctgttatcaaccttgtttatgttcagcagatgcattcacatgcaccatattttatacaactatataatatgacatgcttattaaagacgtgaatatatgcaattttgtctttcttcatttgcttgatgaatgggttctgcttgagcttgtatacattatgatat-gtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
|| |||| | | | | || ||| | ||||| ||||| | ||| | |||| || | | | | | || |||||||||||||||||||||| || || || |||||||| |||||||| ||||||||||| ||||||
------------------------------------------------------------------------------------------aataataaatattttgacctgcatgtttcccattttatgcattt--cagatgattattttccaaatatatagttatattttcttttcttgcccgtgttctagAATGGGAAGCAAATGGTTCAAGAAGGAGCATTGACAGCCTTAGCATCTGTTGCTGATTCTTCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatgaatgggttctgcttgagcttgtatacattatgatatgtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
gcttgat putative branch site (score: 5)
tatacattatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatcaaagctcctgttatcaaccttgtttatgttcagcagatgcattcacatgcaccatattttatacaactatataatatgacatgcttattaaagacgtgaatatatgcaattttgtctttcttcatttgcttgatgaatgggttctgcttgagcttgtatacattatgatatgtgtgaaatccagAATGGGAAGCAAATGGTTCAGGAGGGGGCTTTGACAGCTTTAGCATCAGTTGCTGATTCATCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT