Sequence
atgc intronic sequence ATGC exonic sequencegtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 21
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttca--ttattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
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---------------------------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatt-taaatgcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttca--ttattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
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---------------------------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatt-taaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 19
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
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-------------------------------gtatgtacatccttgaa-gtcactgtt--attttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtat--gtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 19
gtacaattactgtaaggagttatttatt-tatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
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--gtatttgttgtgacttgtaaagtgtggtattta---atttttatgattctcattggagtgtatttcaaatctttctacgctgatatc----aaacatgaatttcttatgttatcct-tcttg---ctatagGTGAATCCAGGAAATGCTCCTCTAGTTGTTGGACAATTATTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTTATACTTTCAGTTCGTTCTCTTC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 21
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
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--gtatttgttgtgacgggtggtat-ttaatttttatgattctcaatataggagtgtat-----tttaaatctttccaggctgatatc----aaacatgaatttcttatgttatcct--tcttgctt--tagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 21
gtacaattactgtaaggagttat--ttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
||| || | | ||| || | || || | | | || | || ||| || |||| || | ||| | | | | ||| | | ||| || | ||| || |||| ||||| ||||| ||||| ||||||||||| || ||||| | ||||||||||||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtaactttgttttcagggtttgtgtttgattttgtgatccttgtagcatatgggtgtgcttcaa-atcattcttggaaagt-tttaaaactgtg--acctaaactttgaa----cttctggcttt------tagGTCAATCCTGGAAACGCTCCTCTAGTAGTAGGGCAGTTGTTAGATGATGAATGCCCTGAAGATTTTATTAAAGGTCTTATACTTTCAGTTCGTTCTCTCC
upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 21
gtacaattactgtaaggagttatttatttatttatttatttttccaa-atgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
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gtaaatttgttttcagggtttgtatttgatttttgtgatccttgtagcatgtaggtgtgct-ttaaatcattcttgaaaagttttttaattctgacc-taaactttgaacttc---ttgctttta-------gGTCAATCCTGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAAGATTTTATCAAAGGTCTTATACTTTCAGTTCGCTCTCTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
ctttaat putative branch site (score: 4)
tattttcttttgtctt CT-rich tract
tattttcttttgtctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttcattattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA