Sequence
atgc intronic sequence ATGC exonic sequence...tctagttcctctgtaataatgaagtgaaacaccctttgcccatgctactcattgcttgttttcttgttgaaacagttaacgatatcatttttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G173858_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 3'ss of exon 1
------tctagttcctctgtaataatgaagtgaaacaccctttgcccatgctactcattgcttgttttcttgttgaaacagttaacgatatcatttttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA
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aaatgaaatatttgctatggaatgacaattt----tacttaatgctagcact--tggttgtttctttgcttgatgaaacattggatgatgtgcttttcccctgcagGATAATGTCTTTGTTCAGCTTATCTGCACAATCCAATATCGGGTTGTTAAGGAACATGCTGATGATGCATTCTATGAGTTGCAGAATCCCCAACAGCAAA
upper sequence: GRMZM2G173858_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g04399.1 (Oryza sativa), 3'ss of exon 2
tctagttcctctgtaataatgaagtgaaacaccctttg------ccca-tgctactcattgcttgttttc-ttgttgaaacagttaacgatatcatttttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA-
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-------tttcaatga-agtgaaatattattttcattgatggaacttactgtcatttcttgctttttttcgttacttgatggaacttcaatcttcttttcttctgcagGATTA-GTCTTTGTTCAGCTGATCTGCGCAATCCAATACCGAGTCGTGAAGGAACATGCTGATGATGCATTCTATGAATTGCAGAATCCCCAACAGCAAAT
upper sequence: GRMZM2G173858_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G32990.1 (Glycine max), 3'ss of exon 1
-------------------------tctagttcctctgtaataat--gaagtgaaacaccctttgcc-----catgctactcattgcttgtttt---cttgttgaaa-------cagttaacgatatcatt----------tttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA
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gtatttcaattctcaatttctttattctttttattttgtcacattctgttcttaatcataatttgtcaggttcttaataatcgatgatggtgatggtcatggagaaaagaatagcagtgagtgatttttttaaatcttgaattgttttgcagGACAATGTGTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA
upper sequence: GRMZM2G173858_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G28170.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------------tctagttcctctgtaataatgaagtgaaacaccctttgcccatgctactcattgcttgttt----------tcttgttgaaa-------cagttaacgatatcatttttctct----------gcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA
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gtcccaaccatcattttccatttcaattctcaatttcttttttttttttttgtatatatatgaattttgtcagattctgttactttcttagcat-acgcatgtgatttttagttcttaccaattgtgacctaataaggatgaagatgatggagaaaagaggagtagtgagtgattttttatttatttaaattgtggtgcagGACAATGTTTTTGTGCAGTTGCTGTGTTCGATTCAATACCGAGTGATTAAGGAAAACGCTGATGATGCTTTCTATGAGTTGCAAAACCCTCAGGAGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactcattgcttgttttcttgttgaaacagttaacgatatcatttttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA
agttaac putative branch site (score: 3)
tatcatttttctct putative PPT
atatcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctagttcctctgtaataatgaagtgaaacaccctttgcccatgctactcattgcttgttttcttgttgaaacagttaacgatatcatttttctctgcagGATAATGTCTTCGTCCAACTGATCTGCACAATCCAGTACCGTGTTGTCAAGGAAAATGCAGATGATGCTTTCTATGAGTTGCAGAATCCCCAGCAGCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - aaacacc
- - - - - - - - - - - - - - - - - - - - - tgctact