Sequence
atgc intronic sequence ATGC exonic sequence...ctttatgtagatttttacttatgtacatggtgttaattcggatatggaattggagatccattaaattttagctcattttttgtactttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 9
-----------------ctttatgtagatttttact--tatgtacatggtgt----taattcggatatggaattggagatccattaaattttagctcattt----tttgtactttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
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gttctgatttctgagccctttctctaaacatgtgttgctctgagcttaatctcacccagtttgcccttatgatttctagatcgtagtgtgttgccttgttaaacattcatagtttccctctttacagGCGCCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 9
--ctttatgtagatttttacttatgtacatggtgttaattcggatatggaattggagatccattaaattttagctcattttt-tgtactttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
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agttatatattggaaactgatatcgtccaaagaatc---ttatatacttgaagagaggagaatgccgctttagccagctttaacaatcatttcctctttacagGCACCATGCATTGTTTTCATTGATGAAATAGATGCTGTGGGATCAACTAGGAAACAGTGGGAAGGGCACACAAAGAAGACATTGCATCAACTTCTTGTTG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 1
--------ctttatgtagat--ttttactta--tgtacatggtgttaattcgg----atatggaattggagatccattaaattttagct------cattttttgtactttcttatttca-tagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
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gtctgttgatttttgcaaatggtatccctaaattgtttgttattctggttttgcactataccacatgggtcctttatttatttctgattatggaatatttatttcccttttatctttctctagGCTCCTTGTATTATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 9
-----------------------ctttatgtagatttttacttatgtacatggtgttaattc-ggatatggaattggagatccattaaattttagctcattttttgtactttcttatttc-atagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
|| | | || ||| | || ||| || | | || | | || | || | |||| ||| | | | ||| ||||||||||| || ||||||||||||||||||||||||||||| || || | || ||||||||||| |||||||| || |||||||||||||| |||||||
gtttgttgcctttggtcaatggcctctcaactgtttgttattctggtttgctaaattacttttgtacataatttccttatttgtttctaattagggacattctttttgccccatcctttttgtagGCTCCTTGTATTATTTTCATTGATGAAATAGATGCTGTTGGTTCAACTAGGAAACAATGGGAAGGTCATACAAAGAAGACATTGCACCAACTACTTGTTG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 9
--------------ctttatgtagatttttacttatgtacatgg---tgttaattcggatatggaat-tggagatccattaaattttagctcattttttgtactttcttatttc-atagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
| ||| || | || | | || || || || |||| | | | | ||| | | |||| || |||| | |||| ||||||||||| || ||||| ||||||||||| |||||||||||||| ||| |||| |||||||| ||||| ||||| || |||||||| || || |||||||
gtctgttgacttttgctaatggtatccttaaattgtttgcaaaagaaggtctgttgtgacatgggtcctttatttttttctgattatggaatatttatttcccttttatctttctgtagGCTCCTTGTATAATTTTTATTGATGAAATTGATGCTGTTGGATCAACAAGAAAACAATGGGAGGGCCACACAAAGAAGACATTGCATCAGCTACTTGTTG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 9
-ctttatgtagatttttact-tatgtacatggtgttaattcggatatggaattggagatccattaaattttagctcattttttgt-actttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
| | | || | ||| | | | |||| | | | | | | | | ||| | || ||| | || || | | | | |||| ||||| || ||||||||||| ||||| |||||||||||||| ||| |||| ||||||||||| |||||||| || |||||||| ||||| |||||||
gtatgactcaacttgtcactgcttatcagctattttaaaagagtttggttgattaggctaccatgaatgaacttttatatttaatgacgatcatgtgttacagGCACCTTGTATTATTTTCATTGACGAAATTGATGCTGTTGGATCCACAAGAAAACAATGGGAAGGGCATACAAAGAAGACATTGCATCAACTACTTGTTG
upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S9_238V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------ctttatgtagatttttacttatgtacatggtgttaattcggatatggaatt----ggagatccattaaattttagctcattttttgtactttcttatttc-----atagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
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gtacatttcgtataaaccaatacccttgtataatattctcttttacactctcgtattcattcttcaaaagaatctgcatatatgatttgctggttttacagagaacttcagttctgtggttttgattgattgtttgtggcgacagGCTCCTTGCATCGTCTTTATTGATGAAATTGATGCTGTTGGGGGCAGCCGCAAGCAATGGGAAGGCCATACGAAAAAAACTCTGAATCAGTTGCTGGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaattggagatccattaaattttagctcattttttgtactttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
ttttttgtactttctt CT-rich tract
attaaattttagctca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttatgtagatttttacttatgtacatggtgttaattcggatatggaattggagatccattaaattttagctcattttttgtactttcttatttcatagGCTCCTTGCATCATTTTCATTGATGAAATAGATGCTGTTGGATCTACACGAAAGCAATGGGAAGGCCATACAAAAAAAACATTGCACCAACTGCTTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - -tacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattaa