Sequence
atgc intronic sequence ATGC exonic sequence...tgttacgaggatggtgtgttgacaattgggtctgtttataaatattggctttatcaacaattgtgtgctctgacttattttttatttcataacaattcagTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g04860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g45840.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------------tgttacgaggatggtgtgttgacaat--tgggtctgtttataaatattggctttatcaacaattg-tgtgctctgacttatttttta--tttcataacaattcagTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG
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gtaagtggtgaaaatatccttctagtgtttcctctgtttcttactttaaaaatgcaattccacaactacttgtgattgactatgacaattatgaatttatgtgcagaagtaataaactcctgataaatgttgtctaattactgaactttaattattcttcagTCGGGAGTTCACTCATCGTGTAAAATCAATATCAATGGCTAAATTTACTTCTCAAGAAGTTTCTGCTCTTCAAGAAGGGGGAAACGAG
upper sequence: Vv09s0002g04860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------tgttacgaggatggtgtgttg-acaattgggtctgtt--tataaatattggctttatcaacaattgtgtg---ctctgacttattttttatttcataacaattc-agTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG
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gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtgaattattgggcacaccagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
upper sequence: Vv09s0002g04860.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------tgttacgaggatggtgtgttgacaattgggtctgtttataaatattggctttatcaacaat-tgtgtgctctgacttattttttatttcataacaattc-agTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG
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gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatatatgcct-tgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggctttatcaacaattgtgtgctctgacttattttttatttcataacaattcagTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG
tcataac putative branch site (score: 2)
tgacttattttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttacgaggatggtgtgttgacaattgggtctgtttataaatattggctttatcaacaattgtgtgctctgacttattttttatttcataacaattcagTCGGGAGTTCACACATAGAGTGAAATCTGTGTCGATGGCTAAATTTACTTCTCAAGAAGTTACTTCCCTTCAAAATGGGGGGAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - -ataaata
- - - - - - - - - - - - - - - - - - - - - - -tggcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tcaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgc