Sequence
atgc intronic sequence ATGC exonic sequence...tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 2
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattat-tatatttttatct--tgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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---tgcacactgaggttatagcatctctatctactccatccgttccaaaatataagcactgtaatatatgttttagtttgctaactcctcttttcacaaacagCGTTTTGCTGCAGTTATCATGAGAATAAGAGAACCGAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatct--tgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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-cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaat-ttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 3
tctcagttatgatgataatgatataatgtcacatgc-tggtttttgctaagttttctctctattattatatttttatcttgaccct--tttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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-ttctgttat--tcggaatcattaatttgcagatgtattatttgtgctagttctaatggttggtggtatgctgtactgatgtctgtgatgtgtttggttgcagCGTTTTGCTGCTGTCATTATGAGGATAAGAGATCCCAAAACAACTGCACTTATTTTTGCTTCTGGCAAGATG
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
--tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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gatcaacatcttaaccttgttcctattggaggaattttttttctttcccta--tttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 2
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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-------------------------------------------------gtttgtgggagagaggaagttttctaacttaacgct-----ctggaaacagCGTTTCGCAGCCGTGATCATGAGAATAAGGGAGCCCAAGACGACAGCGCTGATTTTTGCGTCGGGAAAGATG
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: EFJ29072 (Selaginella moellendorffii), 3'ss of exon 2
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttt-tatcttgacccttttatctgtaaac-agCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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----------------------------------gtttgtttgtgtt----ctttttttttctcttgtgttttatgacttgtctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
lower sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctct-attattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
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----------------------------------gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctct-tatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaagttttctctctattattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
tcttgac putative branch site (score: 3)
cccttttatct CT-rich tract
ttttctctctattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctctattattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA