Sequence
atgc intronic sequence ATGC exonic sequencegtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGGAGTTACTTTGACAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 18
gtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGGAGTTAC---TTTGACAAA
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---------------------------------------------------------------ggaacgcgcaaagaaaaagatggttgtcaaagtg--cattgttcatgtattcttta--gtaggattattgaactgttcttt-ttac-ctattgtttcctattt-cagGTTCTTGATCACTTGGTTATTCAGAAGCTAAATGCTGAGGGCAGGCTTGAGAAGAAAGAATCCAAAAAGGGTGGCTCCATATTTGACAAG
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA14G03780.1 (Glycine max), 3'ss of exon 20
----------gtaaaccaaacatttctt---tgtctatgcttaaatccttttcttttcatactg----tttatatttaaaagcatg-tctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGG---GGAGTTACTTTGACAAA
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gtatgttaaaaatcattagatatctggtggctgtttttgtttcatctttttttctccaactttggcatcctatatttttatgtttaatgcattttttttccctaaaagacattcaattgcttat-tgccatgccttgaggtcaa-caattt-tatatcatttttcatgtgaacatgttcc----atagGTTCTGGACCACTTGGTGATTCAAAAACTAAATGCAGAGGGTAGACTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
gtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGG---AGTTACTTTGACAAA
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-----------------------------------------------------tatttttatatatttttcccctaaaagacatg------caattgcttattgacatgcc-----ttgaggtcaataattttatgtcatttttcatgtga----atgtgttcc--atagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
upper sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
gtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtct--ctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGGAGTTACTTTGACAAA
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---------------------------------------------------------------agtcaatc-acctgtggatgagataggttcaaaacccaaatttttacttgtatcactttgttatagcaggctgta-actttttttcgt-ccaccattctct------agGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGAAGTAATTTTGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGGAGTTACTTTGACAAA
cactaat putative branch site (score: 2)
tgttttttcttatgtt putative PPT
aatttacatgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGGAGTTACTTTGACAAA
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