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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctccatctgtctctattaagcacaaataattgggcaagatagcaagtagagtttaggttgcaaattaaattataaaagtaatagcaactgcaa...

Basic information

species Glycine max
transcript GLYMA10G35560.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35560.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 8
GGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagt--------cctccatctgtctctatta-agcacaaataattgggcaagatagcaagtagagtttaggttgcaaattaaattataaaagtaatagcaactgcaa
 ||||||||| ||||||||||   |||||| |||   || ||||| |||||||||||  |||||||||| || ||||||||||  || ||   ||| |||||||||        ||| ||  | | | ||||     | |  |  |   || | | |  || || |  | || |      ||  | | |     |  |    || ||  
AGAATATGCACAGAAGATGATTGATGCAATCGATAAAGTACGAGTTAGAGGTGATTCGATTGGTGGTGTGGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtatttaaaccctgcagttatgtttattttgatatatgtcctccagctaaa-ataaactaaa--taagctcatcgtttgcactctc----tgcttatgaccgc--

upper sequence: GLYMA10G35560.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 8
GGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctccatctgtctctattaagcacaaataattgggcaa-gatagcaa-gtagagttta-ggttgcaaattaaattataaaagtaatagcaactgcaa
 ||||||||||||||||||||  |||| |||||| | || ||||| ||||| |||||  ||||||| || || ||||||||||  || ||   ||| |||||||||  |  | || | |   |||     |  |  ||  |    ||| |||    |   |||| |||||   |  ||     ||   |  |||  ||| |  
AGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttgaagctctatg-gttatttttatttgttttagttttgattgcatcacatcctttaaggttgatcagcaacaacaaagtcttttagggacttc--

upper sequence: GLYMA10G35560.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 8
GGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaag----tcctccatctgtctctattaagcacaaataattgggcaagatagcaagtagagtttaggttgcaaatta-aattataaaagtaatagcaactgcaa--------------------------------------------------------------
 ||||||||||||||||||||  ||||||||||||| || || ||||| || ||||||||||| ||||||||||| ||||||||||||||    |||||||| ||      |||  ||| ||||| |    |||| | |      ||      |||  |   |  |  ||  | |  | | ||    |||||  |  || |  |                                                               
TGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactctctctctctctctctctctctcacacacacacacacacacacacaaagatgttgaaaattatagaagacagtttcttaagtaccacaaaattaagaaaatacttggttgtgaattgtgatttgcaaaaacattcttcaaatgattattggattgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|16276418|gb|BI941848.1|BI941848
EST:     GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGT                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|16276792|gb|BI942046.1|BI942046
EST:     GATTCTGTGGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGT                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: GATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|120532705|gb|EH260838.1|EH260838
EST:     GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGT                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|10843361|gb|BF066663.1|BF066663
EST:     GTGATTCTGTTGGTGGTGTTGTGACATGCATTGTGAGGAACTGTCCACGA                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAGCTGGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|33387796|gb|CA851003.1|CA851003
EST:     GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGT                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|16277466|gb|BI942396.1|BI942396
EST:     TGTAACATGCATTGTGAGGAACTGTCCACGT                         GGTCTCGGATCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: TGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|19053065|gb|BM731732.1|BM731732
EST:     GTGATTCTGTTGGTGGTGTTGTGACATGCATTGTGAGGAACTGTCCACGA                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAGCTGGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|19268860|gb|BM885116.1|BM885116
EST:     ACATGCATTGTGAGGAACTGTCCACGA                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAGCTGGCTAAAGCT
genomic: ACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|16282970|gb|BI945300.1|BI945300
EST:     GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGAAACTGTCCACGT                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
EST: gi|208201922|gb|GD997013.1|GD997013
EST:     GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGT                         GGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT
genomic: GTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctc ... tatttctcagGGTCTCGGTTCACCAGTATTTGACAAACTTGAAGCTGAACTAGCTAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaagtcctccatctgtctctattaagcacaaataattgggcaagatagcaagtagagtttaggttgcaaattaaattataaaagtaatagcaactgcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG