Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 20
------gtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
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gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatcta-tgtatta-----tacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAA
upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
------gtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA------
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gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatcta-tgtatta-----tacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 20
-------gtaagtcttgtttgctgtgattaa----atccttgttctg---------gtgctgttcctttgagagctaaacattatctt-ctgtattcggcact--gcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
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gtattattctactgttgtgatcttttattaatgacatcactgtacagagagagaaagagagggttgatt-agaatgcagtttgatgtagctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 9
--------------------------gtaagtcttgtt--tgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcact--gcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
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gtattattttaccgttgtgatattttattaatgatattactgtacaaagagaaagggggggggggggggggtgattagaatgcagtttgatgtag-ctgagttatgcttttggcagCAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG
upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 24
gtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
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--gtacattgtttactatttcttacatgtggaac--atatattcccgcaactaattacgtctatgctgatattaatatggttacagTAATCGAATACCTGAAGCCGCTCTGATGGCGAGATCGTACCTTCCAAGCAAGGTCTCCGAAATAGTGGCATTGTGGAGAAACGATTTGACCAAG
upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
-------------------------------------------------------gtaagtcttgtttgctgtgattaaatccttgttctggtgct-gttcctttga------gagctaaacattatcttctgtattcggcactg-------------cagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
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gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
agctaaa putative branch site (score: 3)
taaacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA