Sequence
atgc intronic sequence ATGC exonic sequence...ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggttggtggtatttaatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
ttgactgatagcatcaatttgag---aattgtgattagaaaatttcattatggttggtggtatttaatgtt-atctggtatttaatggtgttatgtgcct---gcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
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-------gttgcgttaaatttggcccaactgtttcatttcagtataactctattctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------------ttgactgatagcatcaatt-tgagaattgtgattagaaaatttcattatggttggtggtatttaat-------gttatctggtatttaatggt--gttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
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gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
-ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggttggtggtatttaatgtt-atctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
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aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataac-attttttttgtat-caaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------------------ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggt----tggtggtatttaatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
||| || | | | |||| | | |||| | | || || ||| | || ||| ||| ||| ||| || | | | | || |||| | || ||||| || ||| | ||||||||||| ||||||| || || ||||||||||| || || |||||||| ||||| ||||| ||||| || ||
gtatgtatctggcttattccttaatgattggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgtgtatcatatgagggcgcatga-tgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaa--agtaaacaattctgctttctac-tgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------------------------ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggt--tggtggtatttaatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
||| || ||||| | | | | ||| | || | ||| | || ||| ||| | | | || ||| | | ||| || |||| | || ||||| || ||| | ||||||||||| ||||||| || || ||||||||||| || || |||||||| ||||| ||||| ||||| || ||
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggc--tttgaatagtatcatggaaatgttgaatctta---agcaaatcattgtgctttctgc-tgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G02730.1 (Glycine max), 3'ss of exon 2
--ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggttggt-ggtatttaatgtt-atctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
| | || | | || | || | || || |||| | | | | | || || || | | | ||| ||| |||| | || | | || ||| | ||| | |||||||||||||||||| |||||||||| || | ||||| ||| | |||||||||||| ||||||||||||
gaatttcccatttatttagcttaacaact-tggttgattaattaatatgtatacgctagacatatatcattgaattaacaagtaacattgtcatgtatcagCGGCAACTAAGCACCTTACATGGCCTATCAGAATGAAAATTGCAATTGGTGCTGCTAATGCCCTTGCATTTTTGCATGAGGAAGCTTCAAGGCCAGTAAT---
upper sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G02480.1 (Glycine max), 3'ss of exon 2
-ttgactg-atagcatcaatttgagaattgtgattagaaaatttcattatggttggtggtatt-taatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
||| | | | | || | |||| | | ||| || | | | || || || | ||| | ||| | | | ||| |||| | ||| | ||| |||| | ||| | |||||||||||||||||| ||| |||||| || || ||||| ||| | |||||||||||| |||| ||||||
tatgataatgttacttgtacttttaatttgttttgtgtaaaatttaatttatttagttataccattgaattaacaagtaataattaatgtcatgtatcagCAAGAAGTATGCATCTTACGTGGCCAATCAGAATGAAAATTGCAATTGATGCTGCTAATGGCCTTGCATTTTTGCATGAGGAAGCTTCGAGGCGAGTAAT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggttggtggtatttaatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
atttaat putative branch site (score: 4)
tatttaatgttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggttggtggtatttaatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
-tgactga
- - - - - gcatcaa
- - - - - - - - - - - - - - - - -agaaaat
- - - - - - - - - - - - - - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtt