Sequence
atgc intronic sequence ATGC exonic sequencegtatggaagaatctccccctcttttaaaaaaaatatatatttccaataatttcttggcaacttatgctaatgagcaactgaaaacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G014089_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g50100.1 (Oryza sativa), 3'ss of exon 7
gtatggaagaatctccccctcttttaaaaaaaatatatatttccaataatttcttggcaacttatgctaatgagcaactgaaaacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
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gtaagaaaggaaaaact----------gaatgctccaagttctcaa--atttaattgtatattaatgaaataatcagctaacaatgttttcat--------gtcatacca--gGGTTATGATACTTTAGTTGGCCAGCGCGGTACTCAGCTCTCTGGAGGACAAAAACAGAGAATTGCAATTGCAAGAGCCATCCTCAAAGATCCAAAAATCC
upper sequence: GRMZM2G014089_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------gtatggaagaatctccccctctt---ttaaaaaaaatatatatttccaataatttcttggc--aacttatgctaatgagcaactgaa-aacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
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gtgagcctatgattcattcatattcaggtcacagttgaaagagggttcaaatatacatgtctgttagaatgagtccatgaatcactgcatttcaacctcacagacctttgtaataataagagtcatgcaatcaaacaaattcttctcttcttttcatcagtattttgaatcatggtggtgtgtttacagGGGCTGGACACAATGGTGGGTGAACATGGAACGCAGTTATCTGGAGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAATCCAAGAATCC
upper sequence: GRMZM2G014089_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------gtatggaagaatctccccctctt--------ttaaaaaaaatatatatttccaataatttc--ttggcaacttatgctaatgagcaactgaaaacattttttttcttgactgacaaac-------cacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
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gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
upper sequence: GRMZM2G014089_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------gtatggaagaatctccccctcttttaaaaaaaatatatatt----tccaataatttcttggcaac-ttatgctaat--gagcaactgaaaacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
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gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggt--gtgattta---attacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttatgctaatgagcaactgaaaacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
gactgac putative branch site (score: 2)
aaaacattttttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggaagaatctccccctcttttaaaaaaaatatatatttccaataatttcttggcaacttatgctaatgagcaactgaaaacattttttttcttgactgacaaaccacagGGCTATGATACTATGGTTGGGCAGCGTGGCACGCAGCTCTCTGGAGGACAGAAGCAAAGGATCGCGATTGCAAGAGCCATCCTTAAAGACCCCAAGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA