Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
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gtacgtctgttctatcacaaatacactac-atttatcctatattttcttaatctag-tgcaaagttcacttac----ttgaattgatttacttc-atcagGAGTC-AGGAGTTGCTATGACGAGGGTAAGCGTGTCGCA-GAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG
upper sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
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-aatgatcatcgactttaatat-ataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTC-GGAGTTGTTATGATGAGGGCAAGCGTGTTGCA-GAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
upper sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
-gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaac--ttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
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taggaatttg---gaatgaccatcgactttaatatataccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtatgaacagGAGTTC-GGAGTTGTTATGATGAGGGCAAGCGTGTTGCA-GAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG
upper sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttt-tatttaacttttttctat--tagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
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--------------gtaggagtaaacacttatcagcttttaattctca--acttatctg-cgtgtcaattcacattcttataacttggtttctattatgatagGTGTT-AGGAGCTGTTATGATGAAGGCAAGCGTGTTGCT-GAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG
upper sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17446 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
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---------------------------------------gtacgtgcaccagatatttgtc---ttgtct---actgcctgctca--ttgtgccgagcagGTGTT-AGGAGCTGCTACGACGAGGGAAAACGCGTGGCC-GAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG
upper sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ35029 (Selaginella moellendorffii), 3'ss of exon 6
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
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---------------------------------------gtacgtgcaccagatatttgtc---ttgtct---actgcctgctca--ttgtgtcaagcagGTGTT-AGGAGCTGCTACGACGAGGGAAAACGCGTGGCC-GAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcataaattatctttcaagttctcttacagtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
atttaac putative branch site (score: 3)
tttaacttttttct CT-rich tract
ttacagtttttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttacagtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA