Sequence
atgc intronic sequence ATGC exonic sequencegtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os04g35420.1 (Oryza sativa), 3'ss of exon 14
gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
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gtaac-ttgattttca-tagtgtgcacatatatttgttgtttattg--gtgcctcgtgctaattgtgcagg--attgcagGTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAG
upper sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G319573_T02 (Zea mays), 3'ss of exon 11
gtatcattgattattactattttcctgac-ttggtagctgatgacaaccatgtattgacatagtc--actagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
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----------gtaacttaatctttcaaacacctgtgtataacatctattattgggtgttccaatctaataggacaaactgtagGTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAG
upper sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G20070.1 (Glycine max), 3'ss of exon 17
----gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
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gtatatttacttccttgctacggcttgctgcactggttaattgaatgggatcatattttaa---agttggta------tttcagGTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAG
upper sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
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gtactggtttttgctaatgttgttttaattcattga--aaatgttgctgcccattaacattg--------cacatttcagGAATCAACAAGCCTGATGTCCGCTTTGTTATTCATCACTCGCTCCCAAAGTCTATAGAAGGCTATCATCAG
upper sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G60930.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatcattgattattactattttcctgacttgg--tagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
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--gtaattaatggtctctgttatagccactttgattgattgaagtttgctgcctgctaacgttgata---------tttcagGAATCAATAAGCCTGATGTTCGTTTTGTAATTCATCATTCTCTACCAAAGTCCATAGAAGGCTATCATCAG
upper sequence: Vv12s0035g00400.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ17581 (Selaginella moellendorffii), 3'ss of exon 8
gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatag--tcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
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--------------------------------gtaagcccgcataatactaaactgcgtgagcttcacaggaattttgacagGTATCAACAAGCCAGATGTAAGATTCGTCATACATCATTCTATTCCAAAATCAATTGAAGGCTATCACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
tattgac putative branch site (score: 2)
atgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcattgattattactattttcctgacttggtagctgatgacaaccatgtattgacatagtcactagactcattacagGTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG