Sequence
atgc intronic sequence ATGC exonic sequencegtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggag-atctgttttttcttccattttgttatgtatgcatgccttcatatgatggga----atgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
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---------------------------------------------------------------------------ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 4
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
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---------------------------------------------------gtacaaaaccaattgcctggttattgg-aattgaagtctctacttactgccaaatgatttgtttcctatacacatctatctt-----tatgcttacgattttcgaata---attcatagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCTCATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
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----------------------------gtacaaaccaattgcc---tgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcc-----tatacccatctatctt-----tatgcttacgatttctgaata---attcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
upper sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatg---atgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
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-----------------------------------------------------------------------ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaa--ttaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
gtttaac putative branch site (score: 3)
aatgttttttctattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA