Sequence
atgc intronic sequence ATGC exonic sequence...tttagcaaattttagctagctgaatacttcttctagatccttctaaccataaggtgaattggttcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os11g13990.1 (Oryza sativa), 3'ss of exon 3
tttagcaaattttagctagc-tgaatacttcttctagatccttctaaccataaggtgaattggt--tcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
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atctgttattggaatcccgcatgaatgaattgaacctatctttgttat-ataatatgaattcactatccaaattagttacaatgttt--tgaataaatttcagGTTGGGGTTGTGTCCGAGGAGAAATTACTTGATCTTTTAGAGATAGCCATGTCAGCAGACACTGCTGAAACAGTGAAAAGGTCCAGAGAACTGATGGATT
upper sequence: Vv12s0035g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g10670.1 (Oryza sativa), 3'ss of exon 1
tttagcaaattttagctagctgaatacttcttc---tagatccttctaaccataaggtgaattgg----ttcaaacttgtt-tatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
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--------atctctatcgatggaccacatgtctgggtaaagaatgctatcggttatgcaacccataattttcgaaataatggtacttaactcaagtcgtgttttatagGTTGGGGTTGTCTCAGAAGAGAAATTGCTTGATCTACTTGAGATAGCTATGTCATCAGACACGGCTGAAACAGTCAAAAGGTCCAGAGAGCTGATGGACT
upper sequence: Vv12s0035g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G136665_T01 (Zea mays), 3'ss of exon 3
-------tttagcaaattttagctagctgaatacttcttctagatccttctaaccataaggtgaattggttcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
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aacaccctataagattccctctctggctgt-cacgacttggaagttataatggcaatgcaat-atttagatcagtcacacaaactgtacttatgcttt-----acagGTTGGGGTTGTGTCTGAGGAGAAACTCCTTGACCTATTGGAGATAGCCATGTCATCAAACACTGCTGAAACAGTCAAAAGGTCGAGAGAGCTGATGGATT
upper sequence: Vv12s0035g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G117028_T01 (Zea mays), 3'ss of exon 1
tttagcaaattttagctagctgaatacttc-ttctagatc--cttctaaccataaggtgaattggttcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
| | | | | | || | ||| || |||| ||| | | | | | | || ||| | | | | ||| | |||| || |||| |||||||| || || |||||| | || || ||| ||||| |||| |||||| |||||| || || |||||||||||| |||||||||| ||||| |
-atgggcacgctaaatttcttgctttctttattttagaatgacttttgagcgatatatcagtta-ttctatccagataatgactgcaactttcatt-tgaaagGTTGGTGTTGTCTCGGAAGAGAAATTGCTTGATCTTCTGGAGATAGCTATGTCAGGAGACACGGCTGAGACAGTGAAAAGATCCAGAGAGCTGATGGATT
upper sequence: Vv12s0035g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G00620.1 (Glycine max), 3'ss of exon 3
tttagcaaattt-tagctagctgaatacttcttctagatccttctaa--ccataaggtgaattggttcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
| || | || | |||| | ||| || | | | | || | ||| || ||||| | ||| || | ||| | | ||| ||||||| |||||||||||||| ||| || ||||||||||||||||||| ||||| ||||| |||| ||| |||||||||||||||||||| || |||||||
ccaaacatgcatataacagttctaataatgctttta-accttacaaaagttttttggtcaaatggtt--agcttaaaaatatgttttttactacctgcaacagGTGGGAGTTGTTTCAGATGAAAAATTATTGGAACTTTTGGAGTTAGCAATGTCGTCAGATACTGTAGAGACAGTGAAAAGAGCCAGAGAACTGATGGACT
upper sequence: Vv12s0035g01960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G40180.1 (Glycine max), 3'ss of exon 3
-tttagcaaattttagctagctgaatacttcttctagatccttctaaccataaggtgaattggttcaaacttgtttatgttatttatt-ttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
|||||| || | || || | || | | | | ||| || |||| | || | ||| || || ||| ||||||| |||||||||||||| ||| || |||||||||||||| |||| ||||||||||| |||| ||| |||||||||||||||||||| | |||||||
aacatgcaaataacagtt--ctaaaaatacttttaactttacaaaagtgttttggtcaaatggtcatcataaaaacataatgttttttattacctgcaacagGTGGGAGTTGTTTCAGATGAAAAATTATTGGAACTTTTGGAGCTAGCAATGTCATCAGATACTGTAGAGACAGTGAAAAGAGCCAGAGAATTGATGGACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accataaggtgaattggttcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
ttctaac putative branch site (score: 1)
ttatttattttcttt putative PPT
aaacttgtttatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagcaaattttagctagctgaatacttcttctagatccttctaaccataaggtgaattggttcaaacttgtttatgttatttattttctttgctgtagGTGGGTGTTGTTTCAGATGAGAAACTACTGGAACTTTTGGAGTTAGCCATGTCATCAGACACTGCAGAAACAGTGAAAAGAGCCAGAGAGCTAATGGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - -ctagctg
- - - - - - - - - - - - - cttcttc
- - - - - - - - - - - - - - - - - - -tccttct
- - - - - - - - - - - - - - - - - - - - - - aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact