Sequence
atgc intronic sequence ATGC exonic sequencegtattcaacttcccaaaagctttctcttttctgtttccttattcatcatattttgataagttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 3
-gtattcaacttcccaaaagctttctcttttctgtttccttattcatcatattttgataagttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
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gttggtcaaaattttatta--ttattcttttct-tttctagagtacttgcttctggtcaaaatgtt--ttgacctttatatctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
upper sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 9
---gtattcaacttcccaaaagctttctcttt--tctgtttccttatt-catcatattttgataagttgtgaataaaatttcaccaa---ttttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
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gttggacactgttttcatataatatccttttttattcgttggctgattgcttgatgtccaaatggttcttcttttaatctttattataacttttcttcagCATGCTATGCATCACGGTGAGGGCTAAGAACCAGCTTAATGGAGAGTGTACAAGTAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAGCGTTTAGCC
upper sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G02620.1 (Glycine max), 3'ss of exon 12
------------------------gtattcaacttcccaa-aagctttctcttttctgtttccttattcatcatattttgata-----agttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
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gtaccaagctcttgtattttttcttcatttatcatactaagaagatttcttgtctagaacctctgcatcaatatgctttttttcctacaatttttaacaattgcttat--atctgtttcagCCTGCTTTGTGTAACAGTAAAGGCTAAAAATTTGTTGAGTGGCGAATCTACCAAGAGCAAGCTTTGGCTTGTGGATTTGGCAGGTAGTGAGAGACTTGCA
upper sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G33340.1 (Glycine max), 3'ss of exon 9
------------------------gtattcaacttcccaaaagctttctcttttctgtttccttattcatcatattttgataagttgtgaat----aaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
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gtaccaagctcttgtattttttctttttttatcatactaaaaagatttcttgtctagacctctgaatcaatatggttttttttcctataatttttaacaattgcttatatctgtttcagCCTTCTTTGTATAGCAGTAAAGGCTAAAAATTTGTTGAATGGCGAGTCTACCAAGAGCAAACTTTGGCTTGTGGATTTGGCAGGTAGTGAAAGACTTGCA
upper sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 11
gtattcaacttcccaaaagctttctcttttctgtttccttattcatcatattttgataagttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
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gtatcatatatgcct----cttttgctgtcttgtttgaatgtttgccatcacattatgagggttgtttaatattgta--aaccct-tacagCATGCTCTCTATAATGGTGAAAGCAAAGAACCTGATGAATGGTGATTGCACAAAAAGCAAGCTTTGGCTTGTAGATTTAGCTGGAAGTGAGAGATTGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttattcatcatattttgataagttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
ttttgat putative branch site (score: 4)
ttttgttc putative PPT
atattttgataagttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcaacttcccaaaagctttctcttttctgtttccttattcatcatattttgataagttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT