Sequence
atgc intronic sequence ATGC exonic sequencegttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 2
------------gttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttcttt----ttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
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gtacaattttaatgcaacatcttttcctttcagtattttttttggtcaactgaggtgatcatatttatatttcatgtgatgtcagGTTGTTGAGGATGGATATGAGTTCTTTGCCGACAGACAACTTGTCACCATATTCTCAGCTCCAAACTATTGTGGTGAATTTGATAATGCAGGTGCAATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 3
-----------------------gttattgccattcccttattgttccattttttat----aactcatgcagctcacag---atagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
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gtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgtcagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G59160.2 (Arabidopsis thaliana), 3'ss of exon 2
-------------------gttattgccattcccttat---tgttcc--attttttataactcatgcagctcacagatagcttctttttcca---gGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
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gttcgtcgtctacacactgttcgtttctattttactaaagatgtcacggaacttctataaaa-atataactgttgtgtt-tttctttttctaaaagGTTGTAGAGGATGGATATGAGTTTTTCGCCGATAGACAGCTTGTTACGATATTTTCTGCTCCCAACTACTGTGGTGAATTTGACAATGCTGGTGCTATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 2
--gtta--ttgccattcccttattgttccattttttat--aactcatgcagctc--------acagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
||| ||| | | || ||| |||| || |||| | || | ||| ||| ||||||| |||||||| ||||| ||||||||||| ||||| ||||||||| ||||||| |||||||||||||| || |||||||| || ||||| |||||||
gttttaacttgagttatatctgccatttagtttattatgaaaactgtgcaaccttaatttgagtgtattggctctgtttatagGTTGTTGAAGATGGGTATGAGTTCTTTGCAGAAAGACAACTTGTTACAGTATTTTCAGCTCCCAACTATTGCGGGGAATTTGACAACGCTGGCGCAATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G46820.1 (Arabidopsis thaliana), 3'ss of exon 2
----------gttattgccattcccttattgttccattttttataactca----tgcagctcacaga--tagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
||| || ||| || | ||| || || ||| ||||| | || | | |||||||| || ||||| ||||| |||||||| || ||||||||||| || || ||||||||||| ||||| |||||||||||||| ||||| |||||| |||
gttagtacattgtataaatgtttcctctagtttttttgtttgggaaatcgaatctgctgctcaagaacctataatgctcccacagGTTGTAGAGGATGGGTATGAGTTCTTTGCTGATAGACAGCTTGTGACTATGTTTTCTGCTCCAAACTACTGTGGTGAATTTGACAATGCGGGTGCATTGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S39_109V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------gttattgccattcccttattgttccattttttataactcatgcagctcacagatagct--tctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
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tgaccagttgtcttttcatgctgttggtagatctcttcagctgctgtaggttagattctttgtacataatgctgatctgtgcgggatgtcccatgcacagGTTGTGGAGGATGGTTACGAGTTTTTCGCTAAGCGCCAACTGGTCACTATCTTCTCTGCACCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------gttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
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gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccatacttttatattctttgtatactatgctgatctgtgtgggatgttacatacagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ20637 (Selaginella moellendorffii), 3'ss of exon 2
-----gttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
| | | | | | || || || | ||| | |||| || ||| | | ||||| |||||||| ||||| || || || || ||||||| ||||| || |||||||| || |||||||||||||| || || || ||| | || || ||||
gtatgatgctcgtgagttctttctttctcgttgctttgagccccatg----tctgcaataacaa----taacagGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA
upper sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 3'ss of exon 2
gttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
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-gtat-gatgctcgtgagttctttctttattgttgctttgagccccatgtctgcaataacaataac-agGTGGTGGAAGACGGATACGAGTTTTTCGCCAACAGACAACTTGTGACGATATTTTCGGCACCCAACTATTGTGGGGAGTTCGACAATTCAGGCGCTATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
tagcttctttttcc CT-rich tract
attttttataactcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattgccattcccttattgttccattttttataactcatgcagctcacagatagcttctttttccagGTTGTGGAAGATGGATATGAATTCTTTGCAGACAGACAGCTTGTTACAATATTTTCTGCTCCCAACTATTGTGGTGAATTTGATAATGCTGGTGCAATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG