Sequence
atgc intronic sequence ATGC exonic sequencegtacatctcttataccctctatagcaaattgtttacttgctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G342105_T02 (Zea mays), 3'ss of exon 7
--------------------------------gtacatctcttata----ccctctatagcaaattg--tttact--tgctttagtagttttgatgcatgtggcaaaaacaaccttcct---tgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG
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gtgattttctctctcattatttaacaaactaattacaattgatgtagtttccctttgatgaacgttgattctactgccaatccatgagaatgcattcatgttctaattttaatttatttaactgcatgcagGCTGCTAACTGGCTCGATTCTGGCTCATGAGATGATGCATGCTTACCTCCGACTTAAAG
upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G06720.1 (Glycine max), 3'ss of exon 9
gtacatctcttataccctctatag-caaattgttta---cttgctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG
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gtatccttctgatatcgtctattttcaaaatctatagtttttgcatatggaattcactctaatataattcaaggattttatattga---tagGTTATTGACTGGATCAATCCTGGCTCACGAAATGATGCACGCATGGCTTAGACTTAAAG
upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 10
gtacatctcttataccctctatagcaaattgtttacttgctttagtagttttgatgcatgtggcaaaaa-caaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG-----------------------------------------
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gtatccttctgataccatctattttca-taatcta-tagtgtttgcatatggaattcaatggatataattcaagattttatattcatagGTTATTGACTGGATCAATCCTGGCCCACGAAATGATGCATGCATGGCTTAGACTTAAAGGTACTATACTACTATCAGCTTTCCTGTTATCAATACCATGT
upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacatctcttataccctctatagcaaattgtttactt--gctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG
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--gtaaaagaaaaacacttctcaacacactcctaaaccaaatttttgtctttataagatatctaa-aattttcgtattacacttgtacagTTTGTTAACCGGGTCAATCCTTGCTCATGAGATGATGCATGCATGGCTTCGACTAAATG
upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ07250 (Selaginella moellendorffii), 3'ss of exon 6
gtacatctcttataccctctatagcaaattgtttacttgctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG-----------------
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-----------------------------------gtgaggggaaacatttcagttctcgccacgaaagactctgatcatgtttgcagTCTGCTCACTGGCTCCATCCTGGCTCACGAGCTCATGCATGCCTGGCTCCGGCTCAACGGTGAGCTCCCTGAACTT
upper sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ07867 (Selaginella moellendorffii), 3'ss of exon 6
gtacatctcttataccctctatagcaaattgtttacttgctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG-----------------
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-----------------------------------gtgagttcag----ttcagttctcgccacgaaacactctgatcatgtttgcagTCTGCTCACTGGCTCCATCCTGGCTCACGAGCTCATGCATGCCTGGCTCCGGCTAAATGGTGAGCTCCCTGAACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacttgctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG
ttttgat putative branch site (score: 4)
ccttcctt putative PPT
aaaaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatctcttataccctctatagcaaattgtttacttgctttagtagttttgatgcatgtggcaaaaacaaccttccttgaatacagGTTGCTGACTGGGTCGATCCTGGCTCACGAGATGATGCATGCATGGCTCCGACTGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG