Sequence
atgc intronic sequence ATGC exonic sequencegtaagataaatgtgtacaagctatatgttgactttcatatttattctggttttaaacttgtttcctgttccactcagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 6
gtaagataaatgtgtacaagctatatgttgactttcatatttattct--ggttttaaact---tgtttcctgttccact-cagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
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---------gtggg-acatgttatttgatgtcccatgtgtcaagtcatgagttttcatctaaatgttttttttcctgttatagGATGACGGGGAGATGTATGATGAATTTGGCAACCTCAAAAAGAAATTCCGTGCTAAAACACAGCAAACTGAAAATGCACCAACCCTTCCTGGGTCTGGAC
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 6
gtaagataaatgtgt--acaagctatatgttgactttcatatttattctggttttaaacttgtttcctgttccactcagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
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gtgggatatgttatttgatgtcccatgtgtgaagtcttaggtttgc----gtctaaatgttgctttc-gttgta----gGATGACGGAGAGATGTATGATGAATTTGGCAACCTCAAAAAGAAATTTCGTGCTAAAACACAACAAACTGAAAATGCACCAACTCTTCCTGGGTCTGGAC
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 5
----------gtaagataaatgtgtacaagctatatgttgactttcatatttattctggttttaaacttgtttcctgttccactcagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
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gtaagattgattaaaatcagatcgtacatgctatatatatatatatatattacctttgtcttataatatcctttttactgg---cagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTAAAGAAAAAATTCCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G11060.1 (Glycine max), 3'ss of exon 5
gtaagataaatgtgta--caagctatatgttgactttcatatttattctggttttaaact-tgtttcctgttccact--cagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
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gtaagattgattaaaagtcagatcatacatgctatataatatatatactacctttgtcttataatatcttttttactgtcagGATGATGGGGAGTTGTATGATGAATTTGGAAATCTTAAGAAAAAATACCGTGCCAAAACACAGCAAGCTGAAGCTGCACGTGGGCTTCCTGGTTCAGGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgttgactttcatatttattctggttttaaacttgtttcctgttccactcagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
tgttgac putative branch site (score: 3)
cttgtttcctgttcc putative PPT
actttcatatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagataaatgtgtacaagctatatgttgactttcatatttattctggttttaaacttgtttcctgttccactcagGATGACGGTGAGTTGTATGATGAATTTGGAAATCTCAAAAAGAAGTTCCGTGCCAAAACGCAGCAAGCCGAAGCTGGACAGGTGCTTCCAGGTGCTGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA