Sequence
atgc intronic sequence ATGC exonic sequencegtaaacatattgatgctcagctttcatcaattgtcatcacaacctcattcttcttcactttagaaattgtaaaattgcaactcagtcttggagcatttgctttgtttccaactttccatttcatttggaagttattaactgcaatatttttctttggattcaatccatcccccttaatggcttcttaaacatgtaacagATGGAGAAGTGGAGAGCTTCAGATTGATCCCTGTGTCACAGGTTGCAGATGTTGTACGGAGGACACACTTTTTCAAGGCAAATTGTTCTCTTGTCATCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04320.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os09g15340.1 (Oryza sativa), 3'ss of exon 7
gtaaacatattgatgctcagctttcatcaattgtcatcacaacctcattcttcttcactttagaaattgtaaa-attgcaactcagtcttggagcatttgctttgtttccaactttccatttcatttggaagttattaactgcaatatttttctttggattcaatccatcccccttaatggcttcttaaaca--tgtaacagATGGAGAAGTGGAGAGCTTCAGATTGATCCCTGTGTCACAGGTTGCAGATGTTGTACGGAGGACACACTTTTTCAAGGCAAATTGTTCTCTTGTCATCAT
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--------------------------------------------------------------------gtaaacattcccatttggc---agaacaaaaactt-gaccccaaccatgctatacttct-----ctgttctctataa-atggtactctagcatgaaaatat-----ttaatgaatcttctaccaactcttgcagATGGAGAGGTTGGTAGCTTCAGATTAATCCCTGTACCACATGCTGCAAATATTATCCGGAGGACACATTTTTTCAAGCCAAATTGCAACCTTGTGATTAT
upper sequence: Vv11s0016g04320.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G08420.1 (Glycine max), 3'ss of exon 7
gtaaacatattgatgctcagctttcatcaattgtcatcacaacctcattcttcttcactttagaaattgtaaaattgcaactcagtcttggagcatttgctttgtttccaactttccatttcatttggaagttattaactgcaatatttttctttggattcaatccatcccccttaatggcttcttaaacatg-taacagATGGAGAAGTGGAGAGCTTCAGATTGATCCCTGTGTCACAGGTTGCAGATGTTGTACGGAGGACACACTTTTTCAAGGCAAATTGTTCTCTTGTCATCAT
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---------------------------------------------------------------------------------------------------------ggtgagccgtacatgttcttca-aatttactg-ttgttatgttctagtggtgccatgatc-accctttgtgataactggtttaataaaatatcaGATGGAGAAGTTGATAGCTTCAAGTTGATCCCTGTTACACAAGTTGCAGAAATCATACGCAAGACACAGTTTTTCAAGGCAAATTGCGCTCTTGTAATCA-
upper sequence: Vv11s0016g04320.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G31960.1 (Glycine max), 3'ss of exon 7
gtaaacatattgatgctcagctttcatcaattgtcatcacaacctcattcttcttcactttagaaattgtaaaattgcaactcagtcttggagcatttgctttgtttccaactttccatttcatttggaagttattaactgcaatatttttctttggattcaatccatcccccttaatggcttcttaaacatg-taacagATGGAGAAGTGGAGAGCTTCAGATTGATCCCTGTGTCACAGGTTGCAGATGTTGTACGGAGGACACACTTTTTCAAGGCAAATTGTTCTCTTGTCATCAT
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----------------------------------------------------------------------------------------------------------gtaagccttacaggttcttc--aatttcactgttgtttttcttctaatggcgccctgttcaccctttgtgataactggtttaataaaatatcagATGGAGAAGTTGATAGCTTCAAGTTGATCCCTGTTACGCAAGTTGCAGAAGTCATACGCAAGACAGAGTTTTTCAAGCCGAATTGCTCTCTTGTAATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttttctttggattcaatccatcccccttaatggcttcttaaacatgtaacagATGGAGAAGTGGAGAGCTTCAGATTGATCCCTGTGTCACAGGTTGCAGATGTTGTACGGAGGACACACTTTTTCAAGGCAAATTGTTCTCTTGTCATCAT
ccttaat putative branch site (score: 4)
ttcttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacatattgatgctcagctttcatcaattgtcatcacaacctcattcttcttcactttagaaattgtaaaattgcaactcagtcttggagcatttgctttgtttccaactttccatttcatttggaagttattaactgcaatatttttctttggattcaatccatcccccttaatggcttcttaaacatgtaacagATGGAGAAGTGGAGAGCTTCAGATTGATCCCTGTGTCACAGGTTGCAGATGTTGTACGGAGGACACACTTTTTCAAGGCAAATTGTTCTCTTGTCATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA