Sequence
atgc intronic sequence ATGC exonic sequence...agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g54170.1 (Oryza sativa), 3'ss of exon 3
agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacag-----gtttattacatatatgatc-tccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
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---tcgttgcctatcggaccaaaataa-gctgtcttgctttcaggcacacgttcatttt--aggaacagaattctgaaatcatttactccttatttactgatacagATATGTGAGTGCGCTGTTATGACTAATCGATTGGAAGTACTTAATCTGTCTGGGAATCGCCTCACAGATGCATGCGGTTCTTACCTTTTCACAATCCTAC
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G472023_T02 (Zea mays), 3'ss of exon 12
agtgctttta-ttattgtatttactcattattgacataacta--taattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
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---gatctcacttattgacccgagtcaacacaaattctcttgctttacagcatatattcagtaaaatgctaagccactttttgcctcgttatttactgaatagATATGTGAGTGCGCTGTTTTGACTGATCGATTGGAAGTACTTAATCTATCTGGGAATCGCCTCACTGATGCATGCAGTTCTTACCTATTCACAATCCTGA
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G32290.1 (Glycine max), 3'ss of exon 13
--agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
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ttcatacaattcttgattaatataataaaagaatgcttttctctttttgcatgactaatctcaaatttgcaaatgta--ttaactttgcttgttcctgtcagATTTGTGAATGTTCACTGCTATTTGCTCGACTAGAAGTGCTTAACATTTCTGGAAACCGTCTTACTGATGCATGTGGATCTTATCTTTCAACAATCTTAA
upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G15560.1 (Glycine max), 3'ss of exon 13
agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctc--------cagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
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-----atctatttatacaattcttgattaatagaataa--aagaatgcttatctatttttgcacgatgaatctcaaatttgcta-atatattaacttgttcctgtcagATTTGTGAATGTTCACTGCTATTTGATCGACTAGAAGTGCTTAACATTTCTGGAAACCGTCTTACTGATGCATGTGGATCTTATCTTTCAACAATATTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
gactaaa putative branch site (score: 2)
tctcc putative PPT
tttattacatatatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
- - - - - - - - - - - - - - - - acataac
- - - - - - - - - - - - - - - - - - - - - -attggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataca