Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagggttcttagaaaattcacatttgcctaaatctccatcttcttggatgtatgattatatttgtcaactgggaatgtagGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------gtaaaagggttctta---gaaaattcacatttgc----ctaaatctccatcttcttggatgtatgattatatttgtcaactgg--gaatg-tagGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
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gtactttttttcatgttttataatgtgtaatatagccattcattgaaccatcaactgtagtacctaaacttctcttatttgaatgtctaaaactgtggtacctaaacttctcttacttgaatgcctaaccaacatcttctatcaaccgaatgatagGGAGGTGGAAGATCATCAGCAAGAGAGACCATTGGAAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTTAAGCTCAAATCTGGAGTAGAG
upper sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------------------gtaaaagggttcttag--aaaattcacatttgcctaaatctcca--tcttcttggatgtatgattatatttgtcaactgggaatg-tagGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
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gtaccttttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG
upper sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 5
gtaaaagggttctt-------agaaaattcacatttgcctaaatctccatcttcttggatgt-atgattatat-ttgtcaactgggaatgt---agGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
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gtactaagtttttttagtgtaatgagtctaacatttttattcaatgtgatatgtatatgtattatgctcatacatcttcattttcttatgtttaagGGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG
upper sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 5
gtaaaagggttcttagaaaattcacatttgcctaaatctccatcttcttggatgtatg-attatatttgt-caactggga------atgt---agGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
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gtactgatttttttagtgtaatgagtctaacatttttattcattgtaatatgtatatgtattatgctcatacatctgatttttcttatgtttaagGGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGACTTTTCTGGAACTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctaaatctccatcttcttggatgtatgattatatttgtcaactgggaatgtagGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
gcctaaa putative branch site (score: 3)
atgtatgattatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagggttcttagaaaattcacatttgcctaaatctccatcttcttggatgtatgattatatttgtcaactgggaatgtagGGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA