Sequence
atgc intronic sequence ATGC exonic sequencegtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 6
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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--------------------------------------------------------------------------gcataattttcatttccat-gtctatctgtaatctcatatgtttt---tcagtcgc-ctaccttacatga-gaatagggaatcacattga-tatttcttaaat------gcagTATCGAATTTGACCGTGATGATGAGCTATTTGCTACTGCTGGAGTCTCAAAGCGCATCAAAGTCTTCGAGTTTTCTACA
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G126795_T01 (Zea mays), 3'ss of exon 7
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgtt--gttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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-----------------------------------------------------------------------------gcacatttgttgtagttctgtgtgcttgccaatcaac-ttcttcacctttattttattgcaa-atattttggatggacatttgattt-----ttttttatatt-----gcagTATTGAATTTGATCGTGATGATGAACTATTTGCTACTGCTGGAGTCTCGAAACGTATTAAAGTCTTCGAATTTTCTACT
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 5
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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----------------------------------------------------------------------------acatttatttccagttctgtgtgctagccaatcaac-tacttcacctttgttttatt---gcaaatatttggta---tgggcatttga-tgtttt---tgttatattgcagTATTGAATTTGATCGTGATGATGAACTATTTGCTACCGCTGGAGTCTCGAAACGTATTAAAGTCTTCGAATTTTCCACT
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S81_234V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgcgttgaaatgcatgctatactatttaattacaattattttttt-aactcccaaggtcagaaaacttt----tcttgatgtcaccctttttgctg--ttgttgaattgttaatttgcattcatcatattaattgtact--tcagtaa-ataatgaacaaactgttga-gttg-agtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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gtgccatatcttgaagccaagcctcttgttctttggtgctgtttttgaactccttgtttcgtagtaggttaagctcatgacctcgtaatatttcctacattgggggtttttcgttttgtaacggtcgagtttctcgtgttaattggtaatgtgttactctcgttactgatattgtaacatatcccttcacattttgaagCATTGAATTTGATCGCGATGACGAGTTCTTTGCGACGGCGGGCGTATCACGGCGTATCAAAGTTTTTGATTTTTCAAGG
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 6
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccct--ttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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----------------------------------------------------------------------------ggcacttagattatactcaattggaaaagcaaattcgcttttgt-atgccacttg----tcggaaattccagtggaaactga------gagtatcactattgcatg--tgcagCATTGAGTTTGGTAGGGATGATGAGTTGTTTGCAACAGCTGGAGTTTCAAGGAGGATTAAAATTTTTGAATTTGCAACG
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttct-tgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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------------------------------------------------------------------------------------gttcatttatatccacgtgtgcgatta-gtttaccttctgatttgtaacttgttgaa-aattcctcatctgt-aaactga-cagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA
upper sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S264_64V6.1 (Physcomitrella patens), 3'ss of exon 7
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtactt--cagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
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--------------------------------------------------------------------------------cgtgctaagcaacacatgaaagatccaca-gtagccaatttcctaatttcacttgttgatcacttatttacgaacttat-agt--agcacttcc-atata----tgcagCATTGAATTTGATAGGGATGACGAATTCTTCGCAACTGCTGGTGTTTCAAGGCGGATCAAAGTTTTTGAATTTGCAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
tttcccatattttctt CT-rich tract
taaataatgaacaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgttgaaatgcatgctatactatttaattacaattatttttttaactcccaaggtcagaaaacttttcttgatgtcaccctttttgctgttgttgaattgttaatttgcattcatcatattaattgtacttcagtaaataatgaacaaactgttgagttgagtatttcccatattttcttgcagTATAGAATTTGATCGAGATGATGAATTGTTTGCTACTGCTGGAGTTTCACGGCGGATCAAAGTTTTTGAGTTTTCCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA