Sequence
atgc intronic sequence ATGC exonic sequencegtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtg-gtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
|| | ||| |||||| || || || | | || | ||| || | || | | | | || | | || ||| | | ||||| ||| ||| | | ||| | || || |||||||| || |||||||| ||||||||||| || ||||||||||| |||||||| ||||||||||||||||||||||| ||||||||| |||| || || |
-------------------gtacactca----tctattcaaacaacccctctctttctgcccttt-tagc-tttgacttatggattctgcgatctctttttagcatttattt-catcttaatttggggcccatgaatcatgatcataagtgataactattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g50080.1 (Oryza sativa), 3'ss of exon 4
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
|| || |||| | | || | | | || || | |||||| ||| ||| || || | | || | ||||||| ||| |||| || ||| | |||||||||||||||| | ||||| ||||||| ||||||||||| |||||||| ||||| ||||||||||| || | || || |||| | |||
-------------------------------------gtagttcctagatac--gccatttgtttccaacagt---accatatatac----tagtgtattagaattaactatccctttta----tcttcacat------------------------gatatagGCATATGACACAATGGTGGGTCAACATGGTGCTCAGCTTTCTGGGGGACAAAAGCAAAGGATTGCCATTGCAAGAGCTATCCTTAAAAATCCAAAAGTCC
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g47490.1 (Oryza sativa), 3'ss of exon 7
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtcta-aacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
| || || || | | | | ||| ||| || || || | || | | | ||| | | | | | | | | ||||| || ||||||||||| ||||| |||||| ||||||||||||| || || |||||||||||||| || |||||||| || | || || || | ||||
--------------------------------------------------------------------gtatgaaagacacagaaatgcttcaacctgtgcgattttt-ttatcgtattgttatttgacaactaactaactaaccatc-tcttctgttttctcagGGCCTGGACACAATGGTTGGTGAACATGGAGCTCAGCTATCTGGAGGGCAAAAGCAAAGAATTGCTATCGCAAGAGCGATCCTTAAAAATCCCAAAATCT
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g35030.1 (Oryza sativa), 3'ss of exon 7
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
||| || | | |||| | |||| | || | | | | | | | | || || || ||||| ||||| || ||||| ||||||| ||||| ||| || ||||| || |||||||||||||| |||||||| |||| ||| | || ||||| || |||
-----------------------------------------------------------------------------------gtacaatgc--caaagtaaaatgttctaattgttaactccatttcagttgttag--ttgacatcatgaaat---atcgcagGGTCTTGAAACGATGGTTGGTGAGCGTGGAATTCAACTGTCTGGAGGTCAGAAGCAAAGAATAGCAATTGCTAGAGTGATTATAAAAAACCCTAGGATCT
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g50100.1 (Oryza sativa), 3'ss of exon 7
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
|| | ||| | | | | || ||||| | || | |||||| ||| || || | ||| | ||| || ||||| ||| || | || || ||| || |||||||| ||||| ||||| || || ||||||||||||||||||||||| | || | |||| |||||
----------------------------------------------------------------gtaagaaaggaaaaactgaatgctccaagttct--caaatt--taattgtatattaatgaaataatcagctaacaatgttttcatgtcatac-----cagGGTTATGATACTTTAGTTGGCCAGCGCGGTACTCAGCTCTCTGGAGGACAAAAACAGAGAATTGCAATTGCAAGAGCCATCCTCAAAGATCCAAAAATCC
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 6
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
| | || | | | | | || | | || | | | || | || | || | || | || | |||||| ||||| || ||| | || || ||| ||| ||||||| || ||||| ||||||||||| || |||||||| |||||||| | || ||||| | |||||
--------------------------------------------------------------------gtacacacataacactatctgttcataccaacacacacctcat------------gtatgaagaactaatcttgtattcacatgattt-----cagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G412276_T01 (Zea mays), 3'ss of exon 5
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
| | || ||| || | | | | | | || ||| | ||| | |||| | ||| || | || |||||| ||||| | ||||| ||||||||||||||||| || |||||||||||||| ||||| || ||||| || ||||| |||||||| ||||| || | |||||||| | |||
------------------------------------------gtataactcaatgaactattacgtccgtaatgctatt-tatttattatatagatgctaattttctgccactcccattgttaatcagtacatct-------------tgtgaaacatccgcagGGTCTTGACACAATGGTGGGGGAACATGGAACTCAGCTGTCTGGAGGGCAGAAACAGAGAATAGCAATTGCTAGAGCAATCATAAAGAACCCTAAGATCT
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G086730_T01 (Zea mays), 3'ss of exon 6
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
| | || || | | | ||||| | | |||| || | | || | | | || || ||||| ||||||||| ||||||||| |||| || || | ||||||||| || ||||| ||||||||||| ||||| |||||||| ||||| || | |||||||| || |||
------------------------------------------------------------------------gtacatataaactaatgcg-gtcataatattaaccttttttttttgccacagattat-taaccagtatattt----tgtgaac--attacagGGTCTTGACACATTGGTTGGGGAACGTGGAACTCAACTGTCTGGAGGACAGAAGCAGAGAATAGCAATTGCTAGAGCAATCGTAAAGAACCCTAGGATCT
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G014089_T01 (Zea mays), 3'ss of exon 6
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggt--gtgattta---attacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
|| ||||| | | || ||| | | || | | ||||| ||||| | || | | | | || ||| || || | | ||| | | | |||||| ||| || ||||| || ||| ||| || ||||| ||||| |||||||||||||| || || |||||||||||||| | || |||| | || |
-------------------------------------------------gtatggaagaatctccccctcttttaaaaaaaatatatatt----tccaataatttcttggcaac-ttatgctaat--gagcaactgaaaacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 6
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
||||| | | || || ||||| || | | || | | | || ||||| || || | | || | | |||| | | | | || ||||| ||||||||||||| || | |||||||||||| || ||||| || || || |||||||| ||||||||||| || ||||||||||||||||||||||
--------------------------------------------------gtatgacattcttttaca-caactgaacca-aaccaagttttatgtttctctctcttttttttctttaagattatttgaag--ttaataaaattgtattat--tctgtttgtagGGAATTGACACAATGGTTGGAGGGCATGGAACTCAACTTTCTGGTGGGCAAAAACAAAGAATAGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
upper sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
| | || || ||||| | |||| | ||| || | | ||| || | | || | | | | |||| | | | | || |||| ||||| ||||||| || || |||| ||||| || ||||| || || ||||||||||||||||||||||| || ||||||||||||||||||||||
-------------------------------------------------------gtgtttaattccaaaatccaaactct---taccttacg--ctagcaactattgcttcaggttgctttcttttatcaagttag--ttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
tgatttaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC