Sequence
atgc intronic sequence ATGC exonic sequencegtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatcagtagagtgttggagaaggcttgcataattggtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatc-agtagagtgttggagaaggcttgcataattg-gtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
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----------------------------------------------------------------------------------------------ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G485898_T02 (Zea mays), 3'ss of exon 14
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacag--ttgttggacatgccttctctacatcatcagtagagt-gttggagaaggcttgcataa----------ttggtatatttatttatttt-----attaacttgtcatcgattttttatttttat--ctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
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------gtattaccctactgcaatttggtttttg-aatgaaagaccctactacaat-tattgtatatttaccatcatcaaacttattaggtaaagat------cataactagtaaaatagatggaagagctgtccataaacagaactgttttgtgtttttaatcttttccttggattaattacatagtgagtgcatgttttctttgctaaagGTTTTTTGTTCAAAAAACGCGCAAAAGCAAATGATTGGAGCAAGCGATGGTTTGTTCTAAATGAGAAAAGTGGAAAG
upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatcag-tagagtgttggagaaggcttgcataattggtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
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--------------------------------------------------------------------------------------tgcatgatttcttcatgtctttttcttctttatcacttaaaactaacttgacaaaactaacttccaaggtagataacaaat-----acttactcttttcattt--agGGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAG
upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatcagtagagtgttggagaaggcttgcataattggtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
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---------------------------------------------------------------------------------------ctttagctttgacctagcgtaggataagtttttgag---gttttagt--ttgttataaaaaccaactgccaaggtcttcaacagaaattttattctgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
tattaac putative branch site (score: 1)
ttttttatttttatct putative PPT
tatttatttattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatcagtagagtgttggagaaggcttgcataattggtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA