Sequence
atgc intronic sequence ATGC exonic sequence...tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttccttttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 3
------------------tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttccttttctgttc-tagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
| |||| | | ||| ||| | | || | || ||| | | ||||| | | | | |||| || || |||| || || | || ||||| | | || ||||||||||||| ||| ||||| |||| ||||| || |||||||| ||||||||||| ||||| | |
gtaaggcagatttcttttttaaccaagatgagtactttatatttaaagataaacttgaaccgttgattttactactactatctgattgagcatgcatcctaaaccttacctttttacagGGCTGAATCACAATCCTTGCATCGGTGGTCTGCCAGGTATTGTCTTCTCCTGCCTGCTCCAAGGTCAACCATTGCAGCTGCATTCAGTCCGGATGGGAGA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 3
tcgtacaaggtttttgcttctgttttcata--caagttttttgcttctgttttctttctttt-tatctttctttctttcttttttgttccttttctgt-tctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
|| | || ||| |||| | |||| | || ||| ||| || || || || |||| | |||||||||| | |||| ||| || | || |||| || | || |||| ||||||||||| |||| || || ||||||||||| ||||| |||||||| |||||||| |||
----actattcttcattgtctattttaactgttgagttacatagttttgtactctcactcttatacctaacttttccctggaatgaaaccttttctgtatacagGGCAGAATCACAGTCCCTGCATCACTGGTCTGCCAAATATTGTCCTCTTTTGCCACCCCCCAGGTCTACTATCGCAGCTGCATTCAGCCCAGATGGGAAA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 2
------------tcgtacaaggtttttgcttctgtttt----catacaagttttttgcttctgttttc-tttctttttatctttctttcttt-------cttttttgttccttttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
| | || | ||| | | ||| | | | | | | | || |||||||||| ||| || ||| ||| | |||| ||| || | || |||| | || |||| |||||| ||||| |||| ||||| ||||| ||||||||||| || ||||||||||||||||||
gtaaggaaagccttttttgagatatttaagaccagtccataatatatcgactactgagtcacatgtgagtctgttcacatctttcttttttttggttggctcgtttaaacctcactgggaacagGGCAGAATCACAGTCCCTGCATAGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G353548_T04 (Zea mays), 3'ss of exon 2
-----------------------tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttc---tttttatctttctttctttcttttttgttccttttctgt-tctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
| |||| | | | | || | | | || | || | ||| | ||||| ||| || | || || | | |||| | |||| ||| || || |||| | | || |||| |||||| ||||| |||| ||||| ||||| ||||||||||| || ||||||||||||||||||
gtaaggatttttttgtctcaatgatattcaagaacagt-ccacaacatattcactactgagtcgcatgtgagtctgttcgcatctttatttttattggctgattcgtttaaacctcactgtgtacagGGCAGAATCACTGTCCCTGCATCGCTGGTCTGCCAAGTATTGCCCTCTTTTGCCACCTCCTAGGTCAACTATTGCAGCTGCTTTCAGTCCAGATGGAAAA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 2
---------------tcgtacaaggtttttgcttctgt-------tttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttccttttctg--ttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
| || || || | | | | | | | ||| || ||||||||| | ||| | | || || || ||||| ||||| || ||||||| |||||| || || | |||||||||| || |||||||||| ||||||||||||||||||||||| || |||||||| |||
gtacttacactaatttagtccataagttatattgaggaaaaagcatgcctttgagaatttgaaattttgttttcttcaagaagagtcaattttggggactaatgtctctgacaatgattttcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGGTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 2
---------------tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttcttttt---------atctttctttctttcttttttgttccttttctgttct-agGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
| || || || | | | |||| | | || | || |||| | || | || || || | || | ||||| ||||| || ||||||| |||||| || || | |||||||||| || |||||||||| ||||||||||||||||||||||| || |||||||| |||
gtactttcacttatttagtccacaagttatatcgaggaaaaagcatgccttttgagaatttgaaattttgctttcttcaagaaaagtcaattttagggactaacttctctgacaatgattatcagGGTTGAGGCTGAGTCATTGCGGCATTTGTCTGCTAAGTATTGTCCTTTGTTGCCTCCTCCAAGGTCTACTATTGCAGCAGCATTTAGCCCAGATGGGAAA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G04140.2 (Arabidopsis thaliana), 3'ss of exon 2
tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttccttttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
|||| || | || | ||| ||||| | | || ||| ||| | | | |||| | ||| ||||| |||||||| ||||||||||||||||| || | || |||||||| | |||||||| ||||| || ||||||||||| || ||| ||||||||| |
--gtacctttcgttcgtcact-tcttcgcttctctttttgatgtgatccctgcctcctttcgggcatctgaatgtaaactgcattccctacatgt---agGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCTAAATACTGTCCTCTTGTACCTCCTCCAAGGTCAACGATTGCAGCAGCTTTTAGTTCAGATGGAAGA
upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G43930.4 (Arabidopsis thaliana), 3'ss of exon 2
tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttcct--tttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
|| | | | |||| ||| ||| || || | | | ||| || || || | || | || | | ||||| |||||||| ||||||||||||||||| || | ||||||||||| ||||||| ||||| |||||||| || || || ||| | ||||||| |
---------------------gtacactt-tatgtttcttgtctct--ttatttgcataggaccttgtttaagctcattgtaattggtgattctttatgaagGGTTGAGGCAGAGTCATTGCAGCATTTATCTGCAAAATATTGTCCTCTTGGAGCTCCTCCAAGGTCAACTATTGCTGCGGCTTTTAGTACTGATGGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttctttctttttatctttctttctttcttttttgttccttttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
tttctttttatctttc CT-rich tract
tttctttttatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgtacaaggtttttgcttctgttttcatacaagttttttgcttctgttttctttctttttatctttctttctttcttttttgttccttttctgttctagGGTAGAGGCAGATTCATTGCAGCATTTATCAGCCAGGTATTGTCCTCTGATGCCTCCTCCGAGGTCTACTATTGCAGCAGCATTCAGTCCAGATGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - tgcttct
- - - - - - - - - - - - - catacaa