Sequence
atgc intronic sequence ATGC exonic sequence...gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
gaaaaaagcataaa--gcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgt---ttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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-attttaatttgaattgtctagggtctgaaatagttcaagcccctaatgactagagttgat----tattgatcttcttactagattagtgattcttatgttttagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 5
gaaaaaagcataaagcatactgtctggagtagttcctg--catcttag---cttggtgactcatctgcttccgatgaccttactaacgtggcaaatct----tgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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-------gggttct-catagtgacttta-tagcttttgagcttgttagatacttggttatttttaatgttctacctggctgaatcaagtaccttctctggtgtgatcagGTACCCAAACCTGAAGAGTGTCAGGGAATTGATCTACAAGAGGGGTTACGGAAAGCTCAACAAGCAGAGGATTCCTCTTCAGAACAACAAAGTCATTGAG
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 5
gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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---------gtaagtgaaa--gttcaacgacattg----attgtcatatggttcattacctgcaccacgggttcttaatat--ttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTAAAAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCCTTAAATGACAACTCTATTGTTGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagct-tggtgactcatctgcttccgatgaccttactaacgtg-gcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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---------------------gtaagtgaaagttcaactacattgattctcatggttcat-tacctgcaccatggttcttaatatttgcaaatccacttcagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaaaaagcataaa-gcatactgtctggagtagttcctgcatctta-gcttggtgact-catctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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-------gtatgtatatacactctcatcctaaaccctttaatctgatgctatgagataacaagagtcttgaagagtgtgact--tttctcttctgtttttcagATTCCCTAACTTGAAGAGTGTCAAGGAATTGATCTACAAGAGAGGTTACGGAAAGCTTAACCACCAGAGGATAGCTTTGACTGACAACTCTATTGTAGAG
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00030.t01 (Vitis vinifera), 3'ss of exon 4
--gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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gtaagtatctcactctttgtttttcttaaaatcctataaaaagtctaaacttgtatagtattcatttgtaatg----tatttatatttcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGCGAGAATTGATTTACAAGAGGGGGTACGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00210.t01 (Vitis vinifera), 3'ss of exon 5
gaaaaaagcataaagcatactgtctggagtagttcctgca----tcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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gtaagtatcttactcttttgtttttcttaaaatcctataaaaagttctgaacttgtgtattattcatttctaatg----tatttatattgcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00090.t01 (Vitis vinifera), 3'ss of exon 3
-gaaaaaagcataaagcatactgtctggagtagttcctgca-----tcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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gggtaagtatcttactcttttgtttttcttaagatcctataaaaagttctgaacttgtatattattcatttctaatg----tatttatattgcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGCGAGAACTGATTTACAAGAGGGGCTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 5
gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgttt-agGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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----------gtatgtgttctgactgcca-acttcataaccttcag--ggatcatatctccacatgcaatc-tgttattcatatactgaagattgtttcagGTATCCCAATTTAAAGAGTGTCAGGGAACTGATTTACAAGAGGGGTTATGGAAAACTTAACAAGCAGAGAACTGCTCTGACTGATAACTCAATCATTGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 4
gaaaaaagcataaagc---atactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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gtaagtatctcactcttttgtttttcttaaaatcctataaaaagtctaaacttgtatattattcatttctaatg----tatttatattgcaaatatt--ttagGTACCCCAATTTGAAGAGTGTGCGAGAATTGATTTACAAGAGGGGGTATGGAAAGTTGAACAAGCAGAGAACTGCCTTGACCGACAACTCCATTGTGGAA
upper sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S11_173V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
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gtaattaaactctggagcaattaataatataagcgtttcg-gtgcctacgaagatgtttttcgcacccctatgtgttagtttaaatttttcacatg-ttttaccatgattgta---cttgc--agCAACCCGAACTTGAAGAGTGTCCGGGAGTTGATCTACAAGCGTGGGTACGGAAATGTAAACAAGTCGCGCACCGCTCTTACGGACAACACCATCATCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
tactaac putative branch site (score: 0)
tcttgttt putative PPT
ttactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaaaagcataaagcatactgtctggagtagttcctgcatcttagcttggtgactcatctgcttccgatgaccttactaacgtggcaaatcttgtttagGTACCCAAACTTGAACAGTGTCAGGGAGTTGATCTACAAGAGGGGCTATGGAAATCTGAACAAGCAGAGGATCCCTCTGTCCAACAACCAAGTCATCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT