Sequence
atgc intronic sequence ATGC exonic sequence...tttatttttttagtatgtgtaggagggatttcccagtcaatggtttccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g10740.1 (Oryza sativa), 3'ss of exon 1
--tttatttttttagtatgtgtaggagggatttcccagtcaatggtttccattttacaagttttttt-catcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
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ggtttttttccctattatta--aatcactatgtcctaggaaagcacctgataattgtagtccttttgatgtcttacaagtaatatcagt-ttgctgtttgcagGCATAGAAATTGATGACGAGGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGATAATAATGGAATTATTACTTTTGAAGAATGGAGGGACTTTCTTTT
upper sequence: Vv17s0000g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g40200.1 (Oryza sativa), 3'ss of exon 1
-tttatttttttagtatgtgtaggagggatttcccagtcaatggtttccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
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cctgaagtcttaaatatattcatagttgggttatttagagattttattgtttgcacatccataatatatcttacaagcaatgtcagcttgt-tgtttgcagGTATAGAGATTGATGATGAGGAGCTTGCACGGTTTGTCGAGCATGTGGACAAGGACAACAATGGAATTATTACTTTTGAAGAGTGGAGGGACTTTCTTTT
upper sequence: Vv17s0000g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G041831_T06 (Zea mays), 3'ss of exon 2
--tttattttttta-gtatgtgtaggagggatttcccagtcaatggtttccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
| || | || || || | ||| || | | || | ||| | ||| | | | | ||| || |||||| | || | || | | |||| || || ||| | ||||| ||||| || | ||||| || |||| |||||||| |||||||| ||||| |||||||||||||||||||||||||||||
gatatactcttctatgtctttgtgaccaggttatttcaagcttcagtta--aatttgtatatataatctatcttacaagcaatgtcagt-ttgctgtctgcagGTATAGAGATTAATGATGAAGAGCTGGCAAGATTTGTTGAGCATGTGGATAAGGACAACAATGGGATTATTACTTTTGAAGAATGGAGAGATTTTCTTCT
upper sequence: Vv17s0000g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G180971_T01 (Zea mays), 3'ss of exon 1
tttatttttttagtatgtgtagg-agggat-ttcccagtcaatggtt--tccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
| | ||| | || || || |||| || ||| | | || | | | | || || ||| | | | || | | ||| |||| || |||||||| ||||| |||||||| | ||||| || |||| |||||||| || |||| ||||| |||||||| || ||||||||||||||| |
--gacactgataggaaacataaatagctatgttccaaggagctggctgataaatctagtctttgtgatatgtcttacaagta-tatcagt-ttaatgtttgcagGTATAGAAATTGATGATGAAGAGCTTGCAAGATTTGTTGAGCATGTGGATAAGGACAATGATGGTATTATTACTTTTGAGGAGTGGAGAGATTTTCTTTT
upper sequence: Vv17s0000g00030.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G041831_T03 (Zea mays), 3'ss of exon 1
----------------tttattttttta-gtatgtgtaggagggatttcccagtcaatggtttccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
| || | || || || | ||| || | | || | ||| | ||| | | | | ||| || |||||| | || | || | | |||| || || ||| | ||||| ||||| || | ||||| || |||| |||||||| |||||||| ||||| |||||||||||||||
ctgctagcgcttttgatatactcttctatgtctttgtgaccaggttatttcaagcttcagtta--aatttgtatatataatctatcttacaagcaatgtcagT-TTGCTGTCTGCAGGTATAGAGATTAATGATGAAGAGCTGGCAAGATTTGTTGAGCATGTGGATAAGGACAACAATGGGATTATTACTTTTGAAGAATGG-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
tgtctcttttttc CT-rich tract
tttacaagttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatttttttagtatgtgtaggagggatttcccagtcaatggtttccattttacaagtttttttcatcctataagcaacagcggtgtctcttttttcagGGATTGAAATTGACGATGAGGAGCTTGCCCGTTTTGTGGAAAATGTTGATAAGGATAACAATGGAATTATAACTTTTGAAGAATGGAGAGATTTTCTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - gtatgtg
- - - - - - - - - - - - - - - -cccagtc
- - - - - - - - - - - - - - - - - - - - - - - ccatttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcaaca