Sequence
atgc intronic sequence ATGC exonic sequence...tgtcaggaaaatttctataattttcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtcttggatgttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 5
tgtcaggaaaatttctataatttt-------cattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtc-ttggat------gttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
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-gtaagaagagtcacttgattctcaaggaaacataaagcagattattattgtcggtgcttctatgccatggtgtcaaaaggaaaataaaatatcattgcattgccccgttgcagGTCTGGGCGTCTCTGTTGTTATACCGGCAAATCCTTGACGAGATAGAAGCAAACGATTACAACAACTTCACAAAGAGGGCGTACGTTGGGAAGGCGAAGA
upper sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G300348_T01 (Zea mays), 3'ss of exon 2
tgtcaggaaaatttctataattttcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtcttggatgttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
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----------------gtaagtccactcaacttcacatttcccacccagtatagcacagcatcctcacttccttttctttg-------ttaccattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCCAACGACTACAACAACTTCACGAAGAGGGCGTATGTTGGTAAAGGGAAGA
upper sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G40720.1 (Glycine max), 3'ss of exon 6
tgtcaggaaaatttctataattttcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtcttggatgtt--gcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
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tggaaaaaagggtcaagccattggccaagggta-atgattttatgcattatttaacaaatttcaaatgtgaactaataagga-tgttgttgatgttttgtagGTATGGGCATCTTTGTTATTGTATCGCCAAATATTGGATGAGATAGAAGCTAATGATTACAACAATTTCACCAGGAGGGCTTATGTGAGCAAAGCCAAGA
upper sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G39050.1 (Glycine max), 3'ss of exon 6
-------tgtcaggaaaatttctataattt-tcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttg-gaatgtcttggatgttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
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gaaaaagggtcaagccattggctaaggctaatgattttatgcattattatt--tagctaatttcaaatgtgaacacaaaagggtgttgtgaatgttttg-------tagGTATGGGCGTCTTTGCTATTGTATCGCCAAATATTGGACGAGATAGAAGCTAATGATTACAACAATTTCACTAGAAGGGCTTATGTGAGCAAAGCCAAGA
upper sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G17230.1 (Arabidopsis thaliana), 3'ss of exon 6
tgtcaggaaaatttctataattttcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaat-gtcttggatgttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
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----gtaagtgtctctaaaacactcttcagccgcaagtttaccgtttacttatttcttttggatcgattttaaccccgaggacttggctgcaatgtttcagGTATGGGCTTCATTGCTATTGTACAGGAGAATACTGGACGAGATTGAAGCGAATGATTACAACAATTTTACTAAGAGAGCTTATGTGGGGAAAGTCAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagatgtttcctgatgtatgttttggaatgttttggaatgtcttggatgttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
tcctgat putative branch site (score: 3)
tatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtcaggaaaatttctataattttcattgggttcattattagcaacagatgtttcctgatgtatgttttggaatgttttggaatgtcttggatgttgcagGTATGGGCATCTTTTCTGTTGTATCGGCAAATACTGGATGAGATTGAAGCTAACGATTACAACAACTTCACTAGGAGAGCTTATGTGAGCAAAGCTAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - -ggaaaat
- - - - - - - - - - - - - - - - - - - - - caacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtc