Sequence
atgc intronic sequence ATGC exonic sequencegtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 5
gtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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gtactcaaaatctgaattctgaacacacaataatatgtatttattttaccacttgttgtgctcattat----gattattcctgttatttgtcaaattccagGGAGCGAACATTCTTGTTGATAACAAAGGATGCATTAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 5
--gtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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gtatgc-acgttgaagtcttaatatataatgcagatatttggccttgtttgttctgttgcaatgcttattctaatg-aacttgaaaattttgccaaatttcagGGTGCAAACATTCTTGTTGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTTGCAAAGTTG
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC197029.3_FGT003 (Zea mays), 3'ss of exon 5
gtgctgtctct-ctttctccccctctctcactctcacttattctctctcttatttcttctttcc--ttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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-----gtatgaacactgaagccttaacatataatggcagatctttggctttgcttgttctgttgaatgcttctaatgaaccttgaaatttt--ccaaatttcagGGTGCAAACATTCTTGTAGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 5
gtgctgtctctctttctccccctctctcactctcactt-attctctctcttatt-tcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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-------------------------gtgaattttatttcattgatatgcatgctatcttggttctttactggcagctgatgttcaagtttttattaatttcagGGGGCCAATATTCTTGTAGATAATAAAGGATGCATAAAACTTGCAGACTTTGGGGCATCCAAACAAGTTGTTGAGCTG
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G39760.1 (Glycine max), 3'ss of exon 5
gtgctgtctctctttctccccctctctcactctcactt-attctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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------------------------gtggatttttatttcattggtatgcatgttatcttgttcttttctggtggctgatgttcaagttttaattaatttcagGGGGCCAATATTCTTGTAGATAATAAAGGATGCATAAAACTTGCAGACTTTGGGGCATCCAAACAAGTCGTTGAGCTG
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G09000.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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---------------gtaacaatttttctccatactttataagtgcttacaatctcgagtccttacccatgagactatatgtttctatgtttt---ctcagGGGGCTAATATCCTTGTGGATAATAAAGGATGCATTAAGCTTGCTGATTTTGGTGCATCCAAACAAGTAGCTGAGTTG
upper sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
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-----------gtacctattgttgtatc-tttgcgtttaaaatatctcgtatccttgccctgcttatctgaggtt--cttctattctcacttt---ctcagGGTGCTAATATCCTTGTGGATAATCAAGGATGCATTAAACTTGCTGATTTTGGTGCGTCCAAACAGGTAGCGGAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
ttttgac putative branch site (score: 3)
atgtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgtctctctttctccccctctctcactctcacttattctctctcttatttcttctttccttcttaggagatgacatgtatttttgacccacatttagGGGGCAAACATCCTCGTCGATAATAAAGGATGCATTAAACTTGCAGATTTTGGTGCTTCCAAGCAGGTTGTGGAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT