Sequence
atgc intronic sequence ATGC exonic sequence...ttgctctttcaagatgcaaatgcaatcttaatattttagatgaggccaaaccatcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g52720.1 (Oryza sativa), 3'ss of exon 6
ttgctctttcaagatgcaaatgcaatctta-atattttagatgaggccaaacca--tcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
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-----------gtatgtatcctcatcctgagacagtattgaatgtgcgatatcaagttaatacgttgctatataatctgaatcttaattaaa--------cagATATACACAGAGAACTGGGTGAATTCACCTGGACAACAGGAAGATAATTCGTGGCAAGCCTTTGTGTACTTACCCCAGGACAGATGGCAAATCATGAAG
upper sequence: Vv09s0002g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G04830.1 (Glycine max), 3'ss of exon 4
------------ttgctctttcaagatgcaaatgcaatcttaatattttagatgaggccaaac-------catcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
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gtgagtgaaatttttcattgtcagggccaaaattttatgctaggaaatctagagggcttaaatttcatttctttggtggtcttgtgagtattgtga-ccgggatga--ttttggtgcagATCTACACAGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAAGCTTTTGTTTATGTGCCTGAAGGCAACTGGTACATTACCAAG
upper sequence: Vv09s0002g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G01410.1 (Glycine max), 3'ss of exon 4
------------ttgctctttcaagatgcaaatgcaatcttaatattttagatgaggc------caaaccatcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
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gtgagtgcactttttcattatcagtgccaaaatgctatgcttggaaatcagaggaattagatttcatttcaggggtggtcttgtgagtattgtga-ccgggatga--ttttggtgcagATCTACACGGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAAGCTTTTGTTTATGTGCCTGAAGGAAACTGGTATATCATGAAG
upper sequence: Vv09s0002g00680.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G01410.2 (Glycine max), 3'ss of exon 4
------------ttgctctttcaagatgcaaatgcaatcttaatattttagatgaggc------caaaccatcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
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gtgagtgcactttttcattatcagtgccaaaatgctatgcttggaaatcagaggaattagatttcatttcagGGGTGGTCTTGTGAGTATTGTGA-CCGGGATGA--TTTTGGTGCAGATCTACACGGAGAATTGGGTCAATTCACCTGGACAGATGGAAGATAATTCATGGCAA------------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaaccatcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
ccttgat putative branch site (score: 5)
ttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgctctttcaagatgcaaatgcaatcttaatattttagatgaggccaaaccatcagttttcttctgaacagtctgaaccttgatgaaatgttggtgcagATATATACAGAGAATTGGGTGAATTCACCTGCACAACAGGAAGATAATTCATGGCAAGCATTTGTTTTTGTACCAAAAGACAACTGGTATATTACAAAG
- - - - - - - - caaatgc
- - - - - - - - - - - - - - - - - - - - - - - caaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaacc