Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatcattgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G017761_T01 (Zea mays), 3'ss of exon 2
gtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatc--attgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
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------------------gtgagtgtttgtttgcgctcggattgg--tttcctgtgcttgtttggattgttga--tgttgttttcttctgtgatt-tacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
gtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatc--attgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
| | | | | || ||| ||| ||||| || | |||||| | | || ||| || | ||| | |||||| | ||| |||| || | ||||||| |||||||| || ||||||||||| |||||||| | ||||||||||| ||||||||||| || || |||
--------------gtgagtgttgtgtttgcgctcggaat-----ggtttcctgtgcttgtttggattgttga--tgttgttttcttctgtgatt-tacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G016330_T02 (Zea mays), 3'ss of exon 2
gtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatc--attgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
| | | | | || ||| ||| ||||| || | |||||| | | || ||| || | ||| | |||||| | ||| |||| || | ||||||| |||||||| || |||||||| || |||||||| | ||||||||||| ||||||||||| || || |||
--------------gtgagtgttgtgtttgcgctcggaat-----ggtttcctgtgcttgtttggattgttga--tgttgttttcttctgtgatt-tacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCACCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 3
gtaagtttttcttaataaacaatttttccgctgcattaattt-cagaatttgctgtgtttaatcattgtt------aaattattatttaattt---tctg-aggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
||||| || || || | ||||| | ||||| | || ||| || ||| | ||||| ||| | ||| ||| | || | || ||| ||| | | | || || |||||||| | ||||||||||| |||| || |||||||| ||||||||||| ||||| ||||||||||| || || ||
gtaagcttcc----atcctcactctttccccccttctaattgactgagtttattgcttttcccccttgttcttttggttttaatctttggtttggatttgtattattcagTCCAACTCATTCTTCAGCGCTTTTCTTTCAATACAACACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAA
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 1
gtaagtttt---tcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatcattgttaaattattatttaatttt-------------ctgaggatgca-------gGCCATATGTTCCGTCCGCTCTTTTCTTCA-AGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
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gtaagccttcattctctccattttacttttcttctgtttc--cttgtgaatatattgt-tttccctatttttaatttattttttggttttaataatcttttgtttgaatttgcattatttagTCCAAGTCATTCATCGGCACTTTTTTTTTCAATACAATACTGCATTGGGACCCCCTTACCGTATTTTGGTGGATACCAACTTCATCAATTTTTCCATCCA-
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 3
-------------------gtaagtttttcttaataaacaatttttccgctgc-----attaat--ttcagaatttgctgtgtttaatcatt---gttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
| | | | | | || ||| | || || || ||| || || |||| | | ||| ||| | | || ||| ||| | | | || || |||||||| | ||||| ||||| |||| || |||||||| ||||||||||| ||||| ||||||||||| || || |||
gtaagcttccattctcactctcactccccccccccccccccccccccttctatcaacgattggtagtttagtgcttttcccctttgctcttttggtttaatctgtggtttggatttgt-attattcagTCCAACTCATTCTTCAGCACTTTTCTTTCAATACAATACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCAATCCAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G26530.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagtt----tttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatcattgttaaattattattt-aattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
||||| | || | | || || | | |||| || || | | | || | || | |||| | | | | ||| ||| |||||| || | |||||||| ||||| || ||||| || ||||| ||||||||||||||||||||||||||||| || ||||| |||
gtaagctatatttgccctccagcaaaaattggtaccttcgtgattttggatcttcttagaaactttggattttgatttgtgattttggtggtgttttgtatcagTCCAAGTGTTCCTTCAGGGCTTTTCTTTTCTCACAACTCTAGTTTGGTTCCTCCTTACCGGGTTTTGGTGGATACCAATTTCATCAACTTCTCTATCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatttgctgtgtttaatcattgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
atttaat putative branch site (score: 4)
ttttctg CT-rich tract
tgtgtttaatcattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatcattgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA