Sequence
atgc intronic sequence ATGC exonic sequencegtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 6
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatg-tagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
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---------gttggattgtgagttaattaataagtttatggaaaattgt----tcttcttatactcatgtgtgttcttacaacagGTATCAAAATTGGCGTTGTCACTGCTATTGCTGCTCCTGCAAGTATTAAGGTGGAGTTTGAAGGGAATGGGGGCCATGCTGGAGCAGTGCTCATGCCTGC
upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G130034_T02 (Zea mays), 3'ss of exon 6
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
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----------gtaggttcccagtaaattaa---catgtttgcgg-tttcaagttgatggtatacaagtct-tctcttacaatagGTATCCCTATTGGCATTGTTACTGCAATTGCTGCTCCTGCAAGTCTTAAGGTGGACTTTGAAGGGAATGGCGGTCATGCTGGAGCAGTGCTGATGCCTGC
upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G34790.1 (Glycine max), 3'ss of exon 6
gtaggcctctttctgttctcattttattcttttcac-agccacaactttcaaaattcccatttat----tggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
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gtacacatcttggagctaacat---agtcatttcattagccataacttcaatgatctgatattctgatgtaatctgtttcttgacccagGTATATCTATAGGCATAGTCACTGCCATTGCAGCTCCAGCAAGTCTAACAGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGTCCTTATGCCTAA
upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G32850.2 (Glycine max), 3'ss of exon 5
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtcta-----tattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
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gtacacatcttggagctaacata--atcattgcattggccataa-tttcaatgatctgatattctgatgtaatatgtttctttacccagGTATATCTATAGGCATAGTTACTGCCATTGCAGCTCCAGCAAGTCTAACGGTTGAATTTGAAGGCAATGGTGGCCATGCGGGTGCTGCCCTTATGCCTAA
upper sequence: Vv05s0020g04900.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G43600.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtaggcctctt-tctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
| ||| || |||| | | ||| | ||| || || | || ||| ||| || ||| || ||||||| ||||||||||| || |||||| | || ||||| ||||||||||||||||| ||||| |||||||| | |||||| |
gtccggttaacttaccttttctgcgtggaagaattttgtgttttttctctctttcattatagttaataagatcatttttgaccacagGTTTAGATATCGGTGTTGTAACCGCCATTGCTGCTCCAGCAAGTTTGAAGGTGGAATTTGAAGGCAATGGAGGTCATGCTGGTGCTGTACTTATGCCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
ttttgat putative branch site (score: 4)
tatattttgatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcctctttctgttctcattttattcttttcacagccacaactttcaaaattcccatttattggtctatattttgatgtagGAATATCTATTGGCATTGTAACTGCCATTGCTGCCCCTGCAAGTATCAAAGTGGATTTTGAAGGCAATGGAGGCCATGCGGGTGCTGTCTTGATGCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG