Sequence
atgc intronic sequence ATGC exonic sequence...ggatttatgtttgtagcataattggttttcaataactttctctacttctctctaatttgttcatgatattagcttctccaataccggttttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0035g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g07912.1 (Oryza sativa), 3'ss of exon 5
ggatttatgtttgtagcataattggttttcaataactttctctacttctctctaatttgttcatgatattagcttctcc--aataccggttttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG
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-------------------gttaggccgtcaattaaaccatatgcttgcattagcttggtacagttagtttgctctacctgaataacgttcatatctctcagCTAGGAGAACTAAGGTGATGCAGAGGCAGTCTACCTTTGTGTTCCATCACACATCTCATCCATGGAGCAAAAATAAAATACTTATTTGGATG
upper sequence: Vv12s0035g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G29080.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------ggatttatgtttgtagca--taattggttttcaa-taactttctctacttc-tctctaatttgttcatgatattagcttctccaataccggtt-ttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG
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gtaaataccatagaatggtactgtattgaacaacgcctttgggaatcttgtcaatgtataaacaaatgattgaggggaaaaccctccaagcttggtgtttttgcttgtttctcaagtaataacttatgcatcatgtatcacaaatcaataatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG
upper sequence: Vv12s0035g00260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G20120.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------ggatttatgtttgtagcataattggttttcaataactttctctacttctctc----taatttgttcatgatat----tagcttct-ccaataccggtt-ttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG
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gtaaatagcatataatggtacttcattgaccaaccactatgggaatcttgtcaatgtataaacgaatgattgagggtacagccctccaagcttggtttttttgcttgtttctcatgtaataacttctgcatcatgtaatatggcctatacttttactaactgttgttcaacagGAAAGAAAATCAAGGTGATGAGGCGGCAGACAACATTTGTTTTCCATCACACTTCTCATCCATGGAGCAGGAGTCCAATCCTAAACTGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctctaatttgttcatgatattagcttctccaataccggttttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG
ctctaat putative branch site (score: 3)
ttttatttt putative PPT
ttttattttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggatttatgtttgtagcataattggttttcaataactttctctacttctctctaatttgttcatgatattagcttctccaataccggttttattttgtagCAAAGGTAAACAAAGAGATGAGGAGACAATCCACCTTTGTTTTCCATCACACATCACACCCATGGAGCAGGAGCCGCATTCTCATTTGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - -tgtagca
- - - - - - - - - - - - - - -caataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctcc