Sequence
atgc intronic sequence ATGC exonic sequencegtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 22
-------------------------------gtgcattgtttttacctgtgtac-cgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
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gtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 22
-----------------------------gtgcattgtttttacctgtgtac-cgtttccattaatattt-ttaattcttattgctttcgttttatcattttgtgttt-tgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
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gtatgattctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgtttcgttgctgatctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
--gtgcattgtttttacctgtgtaccgtttccattaatatttttaatt--cttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
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gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGG-AGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCAT----AATGCTCTGGGTAAAATCATCATAGAC-----------
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----gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
gtgcattgtttttacctgtgtaccgtttccatta-atatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
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-------------gtgtgcaagttttttccaccctgcatccccaaattaccatattatt-ttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 20
gtgcattgtttttacctgtgtaccgtttccatta-atatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
|| |||||| || || | | | | |||| ||||| || | | ||||||||||||| || || || |||||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||||| ||||| |||
-------------gtgtgcaagttttttccaccctgcatccccaaattaccatattatt-ttttctcattgcactttctatgcgcagAAATCGTCTTCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTACATAATGCTCTGGGTAAAATTATCATTGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
|| || | | | || || | || || ||| ||| |||||| | |||| | || ||||||||||| || |||||||| ||||||||||||||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||| || |||
---------------gtgcgtctctctatctttcatctccactatcattgccatgttcatttc-tcatttaattttttatgcatagGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 22
gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
||| | |||| || | | ||| ||| | | || || | ||| ||| || | |||| | || ||||||||||| || || ||||| ||||||||||||||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||| || |||
gtgtgctagttttctctctat----tttgcatctccagt----atcgttgctatgttcatttctcatgttctttttttatgcatagGAATCGTCTCCGATTGCTTACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
-----------gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttg---tttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
| ||||||| ||| || || | | | || | | | || |||| | || ||| || ||| || |||||||| || | | || || ||||| |||||| | || ||||| |||||||| ||||||||||| || |||||||| || || |||||||||||
atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttatagGAATCGTCTGCGACTGTTGACACAATTCTTAGAGCATTTGGTAAGTGAAGGTAGCCAAGATGTGCATGTGCACAATGCTCTTGGGAAGATCATCATAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
ttttaat putative branch site (score: 3)
ttttgttt putative PPT
atttttaattcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG