Sequence
atgc intronic sequence ATGC exonic sequence...ccttggaccatttccttttcattgtcatattttctatatgttcaattcagtagataacatctgcattctttctctgttattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G26960.1 (Glycine max), 3'ss of exon 5
ccttggaccatttccttt--tcattgtcatattttctatatgttcaattcagtagataacatctgcattctttctctgt-tattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
|| ||| | | | ||| ||| || | | | || |||| | ||| || | ||| || | | || | | ||||| ||||||||||||| |||||| | ||| | |||||||||||||||||||||||||| || |||||||| ||||||||||||||||||||||||||| |||||
ggatgtacctgtaagctagataattagcatgttatttct---ttaaatttccgatgtaaatcttgtaatctaatactatgtccattctacattttgtttacagAGGCAACTTATGAAGTGTTACCTAGGCTTAATGAAATAAAATTTGGCAGTGGAGTAATTGATGAACTTTTGTTTCTGGACTTGCCACGTGAAACAAGATT
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G32260.1 (Glycine max), 3'ss of exon 5
----ccttggaccatttccttttcattgtcatattttctatatgttcaattcagtagataacatctgcattctttctctgt-tattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
| | || | || || ||| || || | || || | | || ||| || | | ||| | | | | || ||| | | || |||||||||||| ||||||| | ||| ||||||||||||| |||||||||||||| || |||||||| || |||||||||||| ||||||||||| |||||
ttacctgtaaactagatcattaacat-gttatttcttttaagtttctgatgatgtaaat----ctcgtaatctaataatatgtctgttctgggtttcatttgcagAGGCAACTTATGAAGTATTACCTAGACTTAATGAAATCAAATTTGGCAGTGGAGTAATTGATGAACTATTGTTTCTGGACATGCCACGTGAAATGAGATT
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G32250.1 (Glycine max), 3'ss of exon 3
ccttggac---catttccttttcattgtcatattttctatatgttcaattcagtagataacatctgca-ttctttctctgttattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
||||| | | | | || | | | | | || |||| || ||| || | | | || ||| ||||| |||| ||||||||||||| |||||| | ||| | ||||||||||| |||||||| ||||| || |||||||| |||||||||||||||||||| |||||| |||||
-attggatgtgcctgtaaggtagatgattagcatgttatttctttaaattttttatgtaaatcttgtaactaatactatgtc-cattgtg--cattgtgtacagAGGCAACTTATGAAGTGTTACCTAGGCTTAATGAAATCAAATTTGGAAGTGGAGTGATTGATGAACTTTTGTTTCTGGACTTGCCTCGTGAAACAAGATT
upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G26970.1 (Glycine max), 3'ss of exon 3
ccttggaccatttccttttcattgtcatattttctatatgttcaattcagtagataacatctgcattctttctctgt-tattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
| | || | | ||| | | ||||| | | | | ||| || | ||| ||| | | || ||| | | ||| |||||||||||| |||||| | ||| | ||||||||||| |||||||||||||| || |||||||| || |||||||||||| ||||||||||| |||||
-gtaagtatatgaaaatattgaggtctatctgcccatatggtttgt---ggatgtaaatcttgtaatctaataatgtgtctgttctggatttcgtttgcagAGGCAACTTATGAAGTGTTACCTAGGCTTAATGAAATCAAATTTGGCAGTGGCGTAATTGATGAACTATTGTTTCTGGACATGCCACGTGAAATGAGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagtagataacatctgcattctttctctgttattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
agataac putative branch site (score: 3)
tgttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttggaccatttccttttcattgtcatattttctatatgttcaattcagtagataacatctgcattctttctctgttattttgtggctgttgttaacagAGGCAACTTTTGAAGTACTCCCTCGACTTAATGAAATAAAATTTGGCAGTGGTGTCATTGATGAGCTTTTGTTTCTGGACTTGCCACGTGAATGTAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
ccttgga
- - - -ccatttc
- - - - - - - - - -cattgtc
- - - - - - - - - - - - - - - - - - - - - caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgc