Sequence
atgc intronic sequence ATGC exonic sequence...ctgtgttttctcttcttcttctttctttctcctttcctttttttcagcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 5
ctgtgttttctcttcttcttctttctttctcctt---tcctttttttcagcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
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ttgtacttaaatttatctagaatacttattctcaaaattttagttttctttctccaaaaaggtggcattctaacttgacaaccaatttctacctct---gcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 5
ctgtgttttctcttcttcttctttctttctcctttcctttttttcagcatgtaatagtgtgtc--agctttgataaatgtt-taatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
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--ataatcactgaagagttttcttgatgttcaatagatccattaaaagtattaggtgtttgtttaagtcttctgatatgtcactgttaccccttaat-tgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCACGTTTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 6
ctgtgttttctcttcttcttctttctttc-tcctttcctttttttcagcatgtaatagtgtgtcagctttgataaatgtt-taatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
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-aatcacttaagagctttttcaatgtcctatagattcattaaattttgaaataaattttgtccaagtcttctgatatgccactgttaccccttaat-tgcagTGAACGTGCAGCCTCTGTCAGGGTCTCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGG
upper sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 5
ctgtgttttctcttcttcttctttcttt--ctcctttcctttttttcagcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
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--atgacatcattagcttttctaaggttgagtatattaatttttaaaaatatatattacattgcatgtttcctcatttgtcttttttacccctaatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTGCATTGCTAAAACCTCATGATAGAATCATGGGACTTGATCTACCACATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
gtttaat putative branch site (score: 4)
tcacccttt CT-rich tract
tttgataaatgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtgttttctcttcttcttctttctttctcctttcctttttttcagcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - tctcttc
- - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - - - gcatgta