Sequence
atgc intronic sequence ATGC exonic sequence...ctccaacgttaaccaacataagtaactgcattggagtttgctcataataattacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
Basic information
species | Glycine max |
transcript | GLYMA16G17760.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G17760.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g57220.1 (Oryza sativa), 3'ss of exon 3
ctccaacgttaaccaacataagt----aactgcattggagtttgctcataataattacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
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----aacatgagttcttgggggtccccaaggacaacattttttgctctctgtattcttcacttggactctgactctgtatatatattatgatcttatttgccagGTCTCTTTCCGCACCAAGGTTTTCCACCCGAACATTAATAGCAATGGCAGCATTTGCCTCGACATCCTCAAGGAACAGTGGAGTCCTGCACTTACCATAT
upper sequence: GLYMA16G17760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G102471_T03 (Zea mays), 3'ss of exon 2
---------------------ctccaacgttaac-caacataagtaactgcatt---ggagtt-------tgctcataataa--ttacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
|| || | | | | || | || | ||| ||||| ||| || ||| || | || |||| ||| | | | ||| || | | |||| || |||||||| ||||||||||| || ||||||||||| || || || || ||||||||||| || || || || ||||| ||||| |||| || |
gtattttctctaatttttgatttctaatgccacctctacctgtatatttagattcctagagttacaattgtgcatatggtaacttttgaaacagttacaatgttttaatgtgaagatgatatgcttatctgcagGTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCT
upper sequence: GLYMA16G17760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 3
---------------------ctccaacgttaac-caacataagtaactgcatt---ggagtt-------tgctcataataa--ttacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
|| || | | | | || | || | ||| ||||| ||| || ||| || | || |||| ||| | | | ||| || | | |||| || |||||||| ||||||||||| || ||||||||||| || || || || ||||||||||| || || || || ||||| ||||| |||| ||
gtattttctctaatttttgatttctaatgccacctctacctgtatatttagattcctagagttacaattgtgcatatggtaacttttgaaacagttacaatgttttaatgtgaagatgatatgcttatctgcagGTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTAT--
upper sequence: GLYMA16G17760.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G102471_T04 (Zea mays), 3'ss of exon 3
---------------------ctccaacgttaac-caacataagtaactgcatt---ggagtt-------tgctcataataa--ttacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT-----
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gtattttctctaatttttgatttctaatgccacctctacctgtatatttagattcctagagttacaattgtgcatatggtaacttttgaaacagttacaatgttttaatgtgaagatgatatgcttatctgcaggtgtctttccgcaccaagGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG
upper sequence: GLYMA16G17760.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g01190.t01 (Vitis vinifera), 3'ss of exon 3
--ctccaacgttaaccaacataagt---aactgcattggagtttgctcataataattacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
| | | || || | | | || ||| ||| | | | || | || | | || | ||| | | ||||||| ||| | |||||||| ||||| || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |||||| |||| || |||||||
tttttttatctgtgcctgtatggctttgatttaggatgtgctttagctggaatggtgataaatttgtgtaagaatcttaacaatga-----attgcgtggagcagGTTTCCTTCAGAACAAAGGTGTTCCACCCCAACATTAACAGCAATGGTAGCATCTGCCTTGATATCCTGAAAGAGCAGTGGAGCCCTGCCCTCACAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataattacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
ttatttt CT-rich tract
ttattattttgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctccaacgttaaccaacataagtaactgcattggagtttgctcataataattacaccttgtgggaatgctttgaatgacattcgttattattttgttaagGTTTCATTCCGCACAAAGGTTTTCCATCCTAACATCAACAGTAATGGAAGTATCTGCCTTGACATCCTCAAAGAGCAATGGAGCGCTGCTCTAACAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
ctccaac
- - - - - - ccaacat
- - - - - - - - - - - -aactgca
- - - - - - - - - - - - - - - - -gagtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -caccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacattc