Sequence
atgc intronic sequence ATGC exonic sequence...ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
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-----gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaatacc---gat-tgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 3
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
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---gtatgtgctttcattttgtacctgt-cctatcttttcattcaaatcttggctt-cgtcggatggtaaagattcaaacttttct-----gaactgcagTTGGGGGGCTGTTGAATGCTACCTTTGGCAATGCGACTGAGATGATTATCTCGTTGTACGCATTGAAAAACGGGATGATCCGTGTCGTCCAGCAATCGCT
upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G046480_T01 (Zea mays), 3'ss of exon 4
---------ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttatttttta-------------ttttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
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gtgtgttctttgctcccatgctgtgctacatttcctaaacaaatattagctttaattaacatctgcttagtacttactatttagtaaagatgtaaaaccttttcttttccttctaattgcagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGAGTCGTCCAGCAGTCACT
upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggat-ctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
|||| || ||| | | | ||| | || | |||| | | | ||| | |||||||||||||||| || ||||| |||||||||||||| || |||||||| || ||||| ||||||||||| |||||||| |||||||||||||| |
--------------------------gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT
upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
|| | | | |||| || ||| | | | | | ||| | | | | | | || | | || | || ||||||||||||||| || ||||| || || |||||||| || |||||||| || ||||| ||||||||| | |||||||| |||||||||||||| ||
-------gtatcctcatttattttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
upper sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
---------ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
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taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagct---cctatctctctctctctctcggctaaagaatggtttttttcacttg------cagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
ttctaat putative branch site (score: 2)
tgtttattttttattt putative PPT
ttctaatatgaggtgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- atccaaa
- - - - - - - - - -tgtttcc
- - - - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - - - -tgtcttc