Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g01650.2 (Oryza sativa), 3'ss of exon 5
tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttgcttgagcaagtctattgagtt---tttgttttaatggcctgcagATATGGGCTGGGG---CAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC---
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--------cttgacttcccattccatgattttcataca-ttttagttctcatcttttatcgtgtgtggatcattagggttgaacctaacttagcatttttgttggatagGCTGTGAATTCTAAGAGCATGCTGGATGATTGGCAAGAGAATTTGGCTATTATAACTGCAAACAGGACGAAAGGTGATGATCTTGTAATTACGCACCTTG
upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G104958_T02 (Zea mays), 3'ss of exon 6
tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC------
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--caggagagctgcgtatcattatattagaagga-gaaatcttgttagacacgctcttactttttca---ctgtaatatttgaaactcgtttctgggtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG
upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttg-cttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC---------
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--aacaataaacttcctccaataattgggtcctgaaacaagaagcttgaagtcatgatgacatgattgactttttttgcaatttgtttt-----tttcctgagtcagCCTGGTC---GTAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G41800.1 (Glycine max), 3'ss of exon 7
-------------------------------------tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcatt--cctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC------
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gtaatcctaattggataaactaagaagccatgcaaaatatatcaaatcaagacgtattgttccattgcctcaatagtttcaaaggttatcagtttctaattgatttggaagctcaatcttttgtt---gttgcttttccatccagGTTGGATCCAACGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTAGGTG
upper sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
-------------------------------------tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcatt--cctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC------
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gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgt--tgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggcattcctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC
ttttaat putative branch site (score: 3)
agtttttgttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
tgtgtgg
- - - - - - - - - - -gaaatga