Sequence
atgc intronic sequence ATGC exonic sequence...tatctaggaggttgactttggtgggaattatgatccaaagtagtctcttctgtttggtcaacacttccgaattgtttttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 3'ss of exon 13
-----tatctaggag-gttgactttggtg-ggaattatgatccaa-agtagtctcttctgtttggtcaacacttccgaattgtttttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
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gtaaatatatatcactataaacttttttatagaaagatgatatgctagtattatatttttagttgaaaaaggatctgatccgtctgtaactgta--aatt--cttcagTTGGATGGAAACAGTCATGTAATTTATGCGGAGACAGAAGCTGCTGGTACACGCCTTCTCATCAATGGGAGAACATGCTTATTACAG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G377341_T01 (Zea mays), 3'ss of exon 14
----tatctaggaggttgactttggtgggaattatgatccaaagtagtctcttctgtttggtcaacacttccgaattgtttttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
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gctcttcttagtgcaatgcccacaggctgttttaccctcgtaggtcaactttttttctattaaaaaattttctgatacatctttgtcgta--aatt--cttcagTTGGATGGAAACAGTCATGTAATTTATGCAGAGACAGAGGCTGCTGGTACACGCCTTCTCATTAATGGTAGAACATGCTTACTACAG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
tatctaggaggttgactttggtgggaattatgatcca-aagtagtctctt-ctgtttggtcaacacttccgaattgttt-ttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
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-acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtactt--gagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 16
tatctaggaggttgactttggtgggaattatgatcca-aagtagtctcttctgtttggtcaacacttccgaattgttt-ttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
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-acacagtggtattttatcgataacatcactattttataactggtctgttgttctatatctg-attcttgagttattaactagcagttgccaattgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
tatctaggaggttgactttggtgggaattatgatccaaag---tagtctcttctgtttggtcaacacttccgaa---------ttgtttttgatagtttcagt-ttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
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--gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctgtttggtcaacacttccgaattgtttttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
ttttgat putative branch site (score: 4)
aattgtttttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctaggaggttgactttggtgggaattatgatccaaagtagtctcttctgtttggtcaacacttccgaattgtttttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - tggtggg
- - - - - - - - - - - - - - - - atccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacttcc