Sequence
atgc intronic sequence ATGC exonic sequencegtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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------------------gtaagcactaagcaccagcaacggcaacg--ccatccgtt-----tcaacgacgacgatgt--gcttacgt-----tttggttcgtg------tgcgtgtgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtcc-gttcctgcgc--gcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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-------------------------atttcaagggaccaaaaagt--attttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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-------------tagcaataaactattgcccgtgacttaaa---------atctaatcaaaatcttt-actaaagtgcccgactttgagtctattttattaaataagttttg-acatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgc----gcgcgc-gcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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-----------------------agaactgctgcgggttccatgtcgtc---tacgatg--tattgcgctgtgcagcgttaagtttggtacgt-cctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgc-gcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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------------------------tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttcattacaataatcgc-tgttctgaatgtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ14822 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgc-gcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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-------------------------------------------------------gtgagtggaagtgaattctttggattgatcggtggttctcatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCGTCCCTGCAAGGGGAAGCTCGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGCCA
upper sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgc-gcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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-------------------------------------------------------gtaagtggcagtggatctttgggattgatcggtagttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
ttagattaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgcgcgcgcgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
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