Sequence
atgc intronic sequence ATGC exonic sequence...tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 4
tttcagtttatcttggtaagccttcttatagagaggttcaacatt-taatcatacaccccattca-atttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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---------------gtaactgttgccccttacaatttctttgttctcattgtacttatattttgtatctgttgctgacctttttcttcgtgttcgtt--agGTGGTTATGACACTGAAGATAAAGCTGCGAGGGCTTATGATCTGGCTGCGCTGAAATACTGGGGGCTATCTACGCATATAAATTTCCCG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 2
---------tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgatt--ttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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gtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattagGTGGGTATGACATGGAGGAGAAAGCGGCGAGAGCGTATGACCTGGCGGCGCTCAAGTATTGGGGCCCTTCCACACACATCAACTTCCCG
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 4
-tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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cagacagttaaagatag-atatcattaaataaaatgcttatgacgtcaacaaaggaggaaaattgatgtttattcaagtcattccaaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATCTAGCTGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 4
tttcagtttatcttggtaagccttcttatagagaggttcaacatt-taatcatacaccccattcaatttttcat-catctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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-ttaacttgaagttaaagatatcatttaatattttgctcatgatgatggcaaaagaagaaatataaatgctaatacaagtgat-tccaaaattttactatagGGGGTTATGATATGGAAGAAAAAGCTGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCCCATATAAATTTCCCT
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------tttcagtttatcttggtaagccttcttatagagaggttcaacat-ttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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gtaaggtttcttaagaccttaatatctttttattttcttttaattcaggttgaaattctcagagcttagattaaccagacagttaaagatag-atatcaattaatataaatgcttatgatgttaacaaaagaggaaaattgatgtttattcaagtcatttcgaacttttgattttagGGGGTTATGATATGGAAGAAAAAGCTGCGAGAGCTTATGATCTAGCGGCACTCAAGTATTGGGGACCCTCCACTCACATAAACTTTCCT
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatac--accccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
---tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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aatgcgcagtttacctgggtgagtgtcactcttt-gttgttcg-tgcttgaagttttttttcgttcc-tcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
upper sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 3
---tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
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aatgcgcagtttacctgggtgagtgtcactcttt-gttgttcgtgcttgaagtgttttttcgttcc--tcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAGGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
aactgat putative branch site (score: 3)
attcaatttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatacaccccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
- - - - - - - - - agccttc
- - - - - - - - - - - - - -atagaga
- - - - - - - - - - - - - - - - - - - - - - - - -catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctgaa