Sequence
atgc intronic sequence ATGC exonic sequencegtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------------------------------------gtagcacatatt-cttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
| || | || || | ||| | || || | |||| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || || ||||||||||| | | | ||
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcacatataatatttatttgcagacattcattagttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaat------agGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
|| || || | | | | | | | || | ||||||| || ||||||||||| ||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||
ttgtagttgctagaggttgataatttcttagttttgcaacttgttgcagttaagtgcatcaccactaacaaatgctacttgcttgtactct----tttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------------------------------------------------------gtagcacatattcttcccataaattatgaatttct-----ctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
| || || | || ||||| || | |||||||||| ||||||||||| ||||||||||| ||||||||| | ||||| |||||||||||||||||| |||| || || ||
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatactaattctcgtaaaaattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------------------------------------------------------------gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
| | || | | |||| | | || | ||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| || ||
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactc---gctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------gtagcacatattcttcccataaattatgaatttct--ctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
| |||| || | | |||| | | | |||| ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||||||||||||||| || |||||
aaagttacatagaaaaattaattttgcttttgccgtcttgtattgcttcgaaaaatgaatttctacatcttgt-cacatagttgaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------gtagcacatattcttcccataaattatgaatttct--ctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
|| |||| || || |||| | | |||| ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||||||||||||||| || |||||
aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacat-tttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 3
---------------gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
|| | | | || | | ||||| ||||| ||||| ||||| || || ||||||||||| |||||| ||||||| || |||||| ||||||| || || ||| ||
gtatgtctcattcttttattgttcctgttgctgatgcggtgcgtgtttcta-cagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG--------------------
upper sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ10709 (Selaginella moellendorffii), 3'ss of exon 3
-----------------gtagcacatattcttcccataaattatgaatttctct-cagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
| | | | || | || | | ||| ||||| ||||| ||||| || || ||||||||||| |||||| ||||||| || |||||| ||||||| || || ||| ||
gtatgtctcattcttttattgttcctgttgctgatgcggtgcgtgtttgtttctacagGACAAGTCCTGGCGGGTACGTTATATGGTTGCTAATCAACTATATGAACTCTGTGAAACTGTTGGACCGGAATGTACTAG-------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
tttctctc CT-rich tract
ataaattatgaatttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT