Sequence
atgc intronic sequence ATGC exonic sequence...agagtaatgtgctcacctgtgatctcagaatggaattgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g09920.1 (Oryza sativa), 3'ss of exon 6
-agagtaat-gtgctcacctgtgatctcagaatggaattgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtgg-aattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
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attagtagtagtagtaagggttatttttgtactgatatttttgctcactgtttcctaag---agagtctgtccttctcataagggtttacttcttgattgcagTGCCATGGTTGGTTGCGGCAAACCCTGTCAATTATGGTCGTCCATGTGAATTGTCTTGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
upper sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G114758_T01 (Zea mays), 3'ss of exon 6
-agagtaatgtgctcacctgtgatctcagaatggaattgtcacattc---cttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
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agaacctatgtaatgaagtaggtcctcttttatggcttcatatatgtaaactggagttggatttgttaaatatatttgtgcttta----tttaaataattgcagTACCATGGTTGGTAGCAGCAAATCCTGTGAACTATGGCCGCCCATGTGAACTGTCATGTGTGGAAGCTTTATCAGCAGCCCTCATAATATG
upper sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G14780.1 (Glycine max), 3'ss of exon 6
agagtaatgtgctcacctgtgatctcagaatgga---attgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
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-atttaatctttttgcct-tgtttaaaggttgcctctattgacaatttgacatggaatgcaatgcaata-ataattagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
upper sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G31550.1 (Glycine max), 3'ss of exon 6
agagtaatgtgctcacctgtgatctcagaatgga--attgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
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tatttaatctttttgcct-tgtttaaaggttgcctcattgacaatttgccatggaatgtaatgtaata-atagttagttttcatattttccttttattgcagTGCCATGGCTTGTAGCAGCAAATCCAGTAAATTATGGTCGGCCATGTCAGCTATCTTGTGTAGAGGCTTTATCTGCTGCTTTGACAATATG
upper sequence: Vv07s0031g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 6
agagtaatgtgctcacctgtgatctcagaatggaattgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
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----------------gtaagaacttacgacttaactgataaatatgtatccagatctctaggaaatgtttcta-------atttcttttatggttgcagTACCATGGTTAGTAGCAGCTAATCCAGTAAATTATGGAAGACCATGTGAGTTATCATGTGTGGAGGCTTTATCTGCCGCTTTAATACTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
ttcataatagaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagtaatgtgctcacctgtgatctcagaatggaattgtcacattccttttgtttatcttagagcatgtcttcataatagaaaattgtgtggaattgcagTACCATGGCTGGTGGCAGCAAACCCAGTAAATTATGGTCGACCATGTGAGCTCTCTTGTGTGGAAGCATTATCTGCAGCTTTATTTATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - -aatgtgc
- - - - - - -cacctgt
- - - - - - - - - - - - -cagaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaat