Sequence
atgc intronic sequence ATGC exonic sequence...gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagt-tctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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gccacgttggcaagtgaatatgt-acatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g19290.1 (Oryza sativa), 3'ss of exon 5
gccactctggactacacttcttttatttgaataaaaatc--tcaggtattggatatattttg-agtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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--gtcgatagaaaattgtagaaaaaatggcatggtaatcatttgtttgccaaagagccttggcagtgtgttttttatgtatt-tactttcatgataattgcagGCTTATTCAACAGTTGGTACACCTGATTACATTGCTCCGGAGGTACTATTGAAGAAAGGATATGGAATGGAGTGTGACTT
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G049088_T02 (Zea mays), 3'ss of exon 5
gccactctggactacacttctt--ttatttgaataaaaatc---tcaggtattggat-atattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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--catatggaatggctcagattggtcatctgtttaaaactcatgcctggttctgtttcatatccttgactctattggtgtgcatggttc----atgaaatttatagGCTTACTCTACTGTTGGTACACCTGATTACATTGCACCCGAGGTACTCCTGAAGAAAGGATATGGAATGGAATGTGACTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 5
-gccactctggactacacttcttttatttgaataaaaatctcag-gtattg-gatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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tgtctatcaagattcc-ccccttttccataagcttccttcttgctgcgctgaggtacactt-gagcacagttgacatgtttaatcgcaattt-tgggacacagGCATACTCAACAGTCGGTACACCTGATTATATTGCTCCAGAAGTGCTACTGAAGAAAGGATATGGAACGGAGTGTGACTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
-----gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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tttgcattaatctcctttggaagtttcctattttagttatttatatgacctttccatataatcggagcgtaataag-----atggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------------gccactctggac-tacacttcttttatttgaataaa-aatctcaggtattggatat---attttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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gtatgtttacctcttctttttctgcgcattcttctttcctccaaactactccttgatcgtatggttaataaatggtattccagtacctgcgcgcgagaattcacgcgcgtacattctttttagatatatgacctgtggtttttatttttcgaccactagtcaaacatcaagtattaattccaggttttgctcatcagGCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttga--gtctgttttgt-atttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgt-----tttgtatttatagttctgtcatatgctatc--tagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatg--taggacctgcagctccatgatgttctactactctttgagcatctagttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtc-atatgctatcta---gGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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------------------------------------------------gtgcgtagcttgtacttccttt-tgtcccgatttttatctaagtgttctttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
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-------------------------------------gtgcgtagcttgtacttccttttgtcccgatttttatctaagtttcctttaa--------cagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
ttttgtatttatagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagttctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
gccactc
- - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcat