Sequence
atgc intronic sequence ATGC exonic sequence...ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 13
------------------------ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
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gtaaatcatttcatggtttggttaaattggataaacattgaattgttgccttttattgctaatacatttgactcattttacaattgttgtttcaacaatgtgtatta--tgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 9
-----------------------ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
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gtaatcatttcatggtttggttaaattggataaacattgaattgttgccttttattgctaatacatttgactcattttacaattgttgtttcaacaatgtgtatta--tgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 12
--------------------------ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttgg-----aaaatttagactcattgattggt-ttg----gcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
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gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaa-tccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG
upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G40550.1 (Glycine max), 3'ss of exon 12
---ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
|| | | | | | || | | ||| | || | || || || | | || | |||| | | | ||||||| |||||||||||||||||| || ||||||||||| |||| ||||| ||||||||||||||||| ||| |||||||| || || |||
taactgaaaattcaggtgagctcaattaaaatttcatcattcatttgggagatagacagtttctttctgttccattatttt--ccaaagcaatggtttg-cagTGTGCATCTGGTGGAGCTACGTGGAACTGGTCAATATTTTGCGATGAAAGCTATGGATAAGGGTGTTATGCTCAATCGTAATAAG
upper sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G04850.1 (Glycine max), 3'ss of exon 13
-----ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
| | | |||| | || || | |||||||| | | | ||| ||||| | ||| || | ||| ||||||||| ||| |||||||||||||| || ||||||||||| |||| ||||||||||| ||||||||||| ||| |||||||| || ||||||
tttttttgatttgggtgatagacagtttctttctgtccctttgtttttccaaagctagctt---ctgtggcagtgaatatgatcatatatt-attggtttg-cagCGTGCATCTGGTGGAGCTACGTGGAACTGGTCAATATTTTGCCATGAAGGCTATGGATAAGGGTGTTATGCTCAATCGTAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
cattgat putative branch site (score: 4)
aaaatttaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
- - - ggtatga
- - - - - - - caagtcc
- - - - - - - - - - - - - ctctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaat