Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctat-gcctttctaatttctacttttgttt----cagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
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gtaagtggtaacttagtctgcagttttagacttacaaaaaccaaaagtttgtttgctcatttatttgcaaattctgttggaaaatatggtctggactcttaactca--agaaccattgggctctctatattcttctctcctcgttttgcttatgctttgctatctagcattaaaaacatatatgtttgcttattacagTGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTTGCAAGTTCACTGGAAGCATTTGGAGGGGGGCATAATGATCCAATCAGTGTTGCTTTTGGA
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 3
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttt-taattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
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------------------tatgcctagcgtacaaaacttgtacaaatt----agtttaattattggcattcaataattatataaatttgtgtcaaataattactttatatttatcatgat------agGGAAGGGCTTGGAGAGGCATATGATGGAGACATTTCAATTGCAAGTGCCCTTGAAAATTTTGGAGGAGGGCATAATGATCCTCTATTTGTAACTTTGGGA
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 2
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
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--------------------tactgtacataacttgtcgtataaattagtttaattatatatcagcattccaaattatataaattt-gtgtcaaataattactttata-tttataataat-----agGGAAGGGCTTGGAGAGGCATATGATGGAGACATTGCATTTGCAAGTGCCCTTGAAAATTTTGGAGGAGGGCATAATGATCCTCTATTTGTAACTTTGGGA
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 2
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaat-ttctacttttgt----ttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
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-------------------------------tttctcacagcttatcataacatattgaatattgattt-tgaagatgttagatatgtattttctttatagactttaattgctttacctttgtactttccagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 2
gtaagtgataatgtgtcatttacgtagcatatttgggt-taccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
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------------------ttctcacagcttatcataatatattgaatattga---ttttgaagatgttagatatgtattttctttataggctttatttg---ctttcacttttgtactttc----cagTGAAGGACTTGGGGAGGCCTATGATGGAGATATTGCATTTGCAAGTGCCTTGGAAACTTTTGGTGGTGGGCATAATGACCCAATCAGTGTGGCTTTTGGA
upper sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
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--gtatgctagt-tcaaattttcacagctaattaggattgt---agctctacatttagagttttcttctggctgaaacat-------gtatcttttaacagcgatagattattctttctttttacagTGAAGGACTAGGCGAGGCATACGATGGGGACATTGCTTTCGCAAGTGCACTTGAAACATTTGGTGGAGGCCATAATGATCCAATAAGTGTGGCTTTTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
ttctaat putative branch site (score: 2)
tttctacttttgtttc CT-rich tract
taatttctactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgataatgtgtcatttacgtagcatatttgggttaccaaaacctgaaagttctgtctctgatttgtgaaaagttttaattcagggtttctctatgcctttctaatttctacttttgtttcagGGAAGGACTAGGGGAAGCATATGATGGAGATATTGCATTCGCAAGCTCACTTGAAACATTTGGAGGGGGGCATAATGATCCAATCAGTGTCACATTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG