Sequence
atgc intronic sequence ATGC exonic sequencegttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatggttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G053639_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
gttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatg-gttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
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--------------------------------------------------------------------gcgcacattctaaaaatattagacagcaattt---tttacaaacacatagcaagatatatgtaa-atgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
upper sequence: GRMZM2G053639_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G29520.1 (Glycine max), 3'ss of exon 4
gttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatggttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
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-----------------------------------------------------------------------------gtatgacttt-gcccctaatcttctattttcca----atgccaccttt----cctcaaagaaataatgcctttgcttctctgtgg------cagGTGCACCTAGCTGTTGCTGGTGCTTTCCACACTAGTTTTATGAAACCAGCTGTGTCAAGGTTGGAAGCAGCATTGGCAACAACAGAAATCAGAACCCCAA
upper sequence: GRMZM2G053639_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G06500.1 (Glycine max), 3'ss of exon 7
gttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatggttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
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---------------------------------------------------------------------------------------gtattattttgcccaattttctatttt---ccaatgccacctttcctcaaagaaa---ta-atgcctttgcttctctgtggcagGTGCGCCTAGCTGTTGCTGGTGCTTTCCACACTAGTTTTATGGAACCAGCTGTGTCAAGATTGGAAGCAGCATTGGCAACAACAGAAATCAGAACCCCAA
upper sequence: GRMZM2G053639_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G29490.1 (Glycine max), 3'ss of exon 7
gttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatggttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
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-----------------------------------------------------------------------------gtatgacttt-gcccctaatcttctattttcca----atgccaccttt----cctcaaagaaataatgcctttgcttctctgtgg------cagGTGCGCCTAGCTGTTGCTGGTGCTTTCCACACTAGTTTTATGAAACCAGCTGTGTCAAGGTTGGAAGCAGCATTGGCAACAACAGAAATCAGAACCCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattcttagtattttacgaaaagaatttacatggttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
ggttaac putative branch site (score: 3)
tatttcc putative PPT
aaaagaatttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatggttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT