Sequence
atgc intronic sequence ATGC exonic sequence...atttttattattgaagtccttacaaggtcatgtcgttctagtgtttctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 2
----------atttttattattgaagtccttacaaggtcatgtcgttctagtgtttctatttctttgctaccag----taggaccctctcctgatatacagc--gtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
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ggttcataaaaagttgagcagcaaagtttttaccagttcaagagtttgtactgttaa-atttcactatagcaagcgaataggattcctcttgcttatgcagTATGTGTTTTGCCAGAAATTGCATACAGTTGGCCAATACTTCTTGGTGGGCAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATTTCTATTAGTAG---------------
upper sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
attt-ttattattgaagtccttacaaggtcatgtcgttctagtgtttctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA-
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atatattattatttatattcat-tagcataattttgaactc-cctattttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
upper sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------atttttattattgaagtccttacaaggtcatgtcgttctagtgtttctattt-ctttgctaccagtaggaccctctcctga--------tatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
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gcaagctctcgccttttctcctcttttatatctcta-aagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
upper sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
-atttttattattgaagtccttacaaggtcatgt-cgttct-agtgtttctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
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gaacacctgcatgtgggccc--acagctttgtgtatattctgagcctgtggatctgctttatgctttgccagctgtttcctaac-cagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
tcctgat putative branch site (score: 3)
tgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttattattgaagtccttacaaggtcatgtcgttctagtgtttctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT