Sequence
atgc intronic sequence ATGC exonic sequencegtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g43090.4 (Oryza sativa), 3'ss of exon 3
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggtt--gtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
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----------------------------------------------------------gtaagtggttgcacattctgtttttagtttcatttctcatttcagcattttgttatagattcgtatgtctcttt-caagctggcaattatttaaa--attttgcagGAAACGGCTCTTAACCATGTAAGGACTGCTGGTCTTCTTGGAGATGGTTTTGGGGCTACACCGGAGATGAGCAAACGGAACTTGATATGGGTTGTCAGCA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 2
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggtt--gtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
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----------------------------------------------------------gtaagtggttgcacattctgtttttagttttatttctcatttcagcattttgttatagattcatatgtctcttt-caagctggcaattatttaaa--attttgcagGAAACAGCTCTTAACCATGTGAGGACTGCTGGTCTTCTTGGAGATGGTTTTGGGGCTACACCGGAGATGAGCAAACGGAACTTGATATGGGTTGTCAGCA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 2
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
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------------------------------------------------------gtgatacaatggag--ctatgctgctttagcttttcttccgtatttttcactattggtacattatgttcgtggcatactaact-gtaatttgaagctttg-----cagGAAACAGCTCTGAACCATGTGAAAACTGCTGGTCTCTTAGGTGATGGTTTTGGTGCTACGCCGGAGATGAGCAAACGGAACTTAATATGGGTTGTCAGCA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g39520.2 (Oryza sativa), 3'ss of exon 2
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttga-ttggtgtgtgtaagcctgcttgctc----cttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
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---------------------------------------------------------------------------------------gtgaaatattgtgaattttcaggcgtcggattgctcgggctgggcatcagaacattgaaatgtttttggttttgatgcagGAAACCGCACTGAATCATGTGAAGAGCGCTGGGCTGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCC
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 2
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatga-acactcataaggcatctggttgtttatc-atcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcg-cagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
||| ||| | ||| || || |||| || ||| ||| | | | || || | || | | || | ||| || |||||||| || ||||||||||| | ||| ||||| ||||| || ||||||||||| | |||||||||||||||| | | ||| | || ||||| ||||
--------------------------------------------------------------gtgacacaatgatactacaaaacgtagtttgtctgccttttttgctctatttactattggtctatcttgtttcattgtgcctcgctttattttgaattttcagGAAACAGCTCTTAACCATGTGAAGACAGCTGGCCTTCTTGGAGATGGTTTTGGCGCCACGCCAGAGATGAGCAAACGAAACTTGATCTGGGTTGTCAGCA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G21910.1 (Glycine max), 3'ss of exon 2
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
| ||| | || | | || | | ||| | || | | || | | || | | || | || | ||| | | | ||||| ||||||||||| ||||||| ||||||||| ||||| |||||||| |||||||| ||||| || ||| ||| || |||||| ||||||||||| |||
-------------------------------------------------------atcaaagaacaatgccaaaaacacctatgga-atctaagttttgtgcaattgcttattgatgattttattttatt----gcctaaattgtctgttttccaa--acagGAGACTGCACTTAATCATGTTAAGACTGCTGGGCTTCTTGGTGATGGATTTGGTTCCACGCCTGAAATGTGCAAAAAGAACCTGATATGGGTGGTGACTA
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G08060.3 (Glycine max), 3'ss of exon 2
gtatgaacaa--ttaattcatcacatttatgtggccaaaagaaa-gagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctc---tccttgt---atcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
||| | | | | | || | | || | ||| | ||| || | | | | | | | || | ||| | || | || | | | | | | ||| ||| | ||| || || | | | || | ||| | ||||||||||||||||| ||||||| | |||||| ||||| |||||||| |||||||| |||||||| ||| ||| || |||| | ||||||||||| ||||
gtaagtccgtcctcatacaagtgaatctttatgatcttcagagatgagtatgctttgactaagatagggctgtttatttagtcactg-taattcaatttcatatatagataatatcattctg-ttgttacttttcatactatatttatatcaactatttgcttaacaacagGAAACTGCACTTAATCATGTTAAAAGTGCTGGGCTTCTTGGTGATGGCTTTGGTTCCACGCCAGAAATGTGCAAAAAGAACTTGATATGGGTGGTTACTC
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G12940.2 (Glycine max), 3'ss of exon 2
gtatgaacaa--ttaattcatcacatttatgtg-gccaaaagaaagagaatacccctgtttaaaaatgaacactcataagg---catctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctc---tccttgt---atcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
||| | | | | | || | | || || | | ||| || | | | | || | || | || | || || | | | | | |||| ||| | ||| || ||||| | | || | ||| | ||||||||||||||||| ||||||| | |||||| ||||| |||||||| || ||||| |||||||| ||| ||| || |||| | |||||||| || ||||
gtaagttcgtcctcatacaagtgaatctttatgagcttcagagatgagtatgttttgactaggacagggctgtatatttagttacactgcataattgaatttcatgtatagataatatcatcctg-ttgttacttttcatacttgatttatatcaactatttgcttaacaacagGAAACTGCACTTAATCATGTTAAAAGTGCTGGGCTTCTTGGTGATGGCTTCGGTTCCACGCCAGAAATGTGCAAAAAGAACTTGATATGGGTAGTTACTC
upper sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
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--------------------------------------aatgggaaaaacacctat--ggaaactaagttttgta---caattgcatattgatttattttattttattgtttgaat-tgtttgtttatttaaaaaaacaaa------------------cagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
tttctctccttgtatc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA