Sequence
atgc intronic sequence ATGC exonic sequencegttagttgatatgcatttttatcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgttattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G01270.1 (Glycine max), 3'ss of exon 6
---------------------------------------gttagttgatatgcattttta---tcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgt--tattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
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gttagcttgttgtttatgcatatcttctctggccattttactcactaaaatgcatatgtaaggttttatttaaaaatataaaacttgaggttaaacattgtttcattttcttctttgt-atatagttatcatggtactgcattatttttc--------atttgtttcattttagattaaatt-attaaaatcatagtttatttg-------cagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTAAAGATCACATCTTTGGACTTGTTCTGATGAATGACTGGAGTG
upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G12100.1 (Glycine max), 3'ss of exon 6
gttagttgatatgcatttttatcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgttattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
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--------------------------------------------------------------aatttcttctttgtatatagtttgttctaaatg----agttatcttggtactgcattgtttttcatttattttatttaa-gcttaaaatcttagtttattgg---cagGCTACTATTGTTGGACCTGGAAATGAATTGGGAAAACCTGTTGATATTAACAATGCTGAAGATCACATCTTTGGACTTGTTGTAATGAACGATTGGAGTG
upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G15210.1 (Glycine max), 3'ss of exon 2
gttagttgatatgcatttttatcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgt--tattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
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---------------------------------------------------------------------------gtatatatttatcatgatactgcattacttttctttt--------gtttcaatttagattaaatt-attaaaatcatagtttatttg-------cagGCTACTAATGTTGAACCGGGAAATGAATTGGGAAAACCTGTGGATATTAACAATGCTGAAGATCACATCTTTGGACTTGTTCTGCTCAATGACTGGAGTG
upper sequence: Vv00s0187g00300.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G20850.1 (Glycine max), 3'ss of exon 2
gttagttgatatgcatttttatcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgttattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
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---------------------------------------------------------------------------------gtatatagttatcatgatactgcattatttttcttttgtttcaatttagattaaatt-attaaaatcatagtttatttg-------cagGCTACTAATGTTGGACCGGGAAATGAATTGGGAAAACCTGTGGATATTAACTATGCTCAAGATCACATCTTTGGACTTGTTCTGCTGAATGACTGGAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
tgttaat putative branch site (score: 3)
tatttgttaattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttgatatgcatttttatcctatttaagaattttaaactcatgattaattttagtatcaaattttgtcttatgatgaatttatcgttattgcaccagttgtcttgttgtgatatgtgttgtctctgattctatttgttaattatatggcttatttattgcacccagGCTGCTATAGTTGGTCCTGGTAATGAATTAGGAAAGCCTGTGGATGTTAATGAGGCTGCAGATCACATCTTTGGACTTGTGATCATGAATGACTGGAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA