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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGACTATTAACGGTGATGATTTGCTCTGGGCCATGGCCACTCTTGGTTTTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttgatttacataatttcacttcttttttaatttcaaaagcttttctggtcccccgaaacaaaattgtctaccgtgtggtttttatttttttagggatttctgctgttggattctgggttttactgatagtattttttttattttttttatttatggctttaccgtggtcgaattgggaatgttgcag

Basic information

species Glycine max
transcript GLYMA19G36220.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36220.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 2
AAAGACTATTAACGGTGATGATTTGCTCTGGGCCATGGCCACTCTTGGTTTTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaat-----tttgatttacataatttcacttcttttttaat---ttcaaaagcttttctggtcccccgaaacaaaattgtctaccgtgtggtttttatttttttagggatttctgctgttggattctgggttttactgatagtattttttttattttttttatttatggctttaccgtggtcgaattgggaatgttgcag
 ||||||||||| || ||||||||||||||||| ||||| ||| | || |||||||||||||| ||||| || ||  | ||| |  ||  |||||||||||||||     ||||| || |    |||| |   || ||||     || |     || | || | | | |||   |    || |    |||  || |||||                                                                                                     
GAAGACTATTAATGGGGATGATTTGCTCTGGGCAATGGCGACTTTAGGGTTTGAGGATTATATTGATCCGCTGAAGTTGTACTTGGCTGCATACAGAGAGgtaatatgtctttgactttcgggttttctcgatttgtttagaccattgatgtagttgtttgcttcactgaattgatgccgttttttttgtc-ttgttattc----------------------------------------------------------------------------------------------------
















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|10233651|gb|BE802539.1|BE802539
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|13252330|gb|BG363233.1|BG363233
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|298196320|gb|HO044711.1|HO044711
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAGGGTGATACG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAGGGTGATACG
EST: gi|120491608|gb|EH219775.1|EH219775
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|19271302|gb|BM887558.1|BM887558
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|298195924|gb|HO044315.1|HO044315
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|298164637|gb|HO014282.1|HO014282
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAGGGTGATAC
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAGGGTGATAC
EST: gi|19347223|gb|BM892103.1|BM892103
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|120491468|gb|EH219635.1|EH219635
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTCCCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|7639292|gb|AW733618.1|AW733618
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|10234684|gb|BE803572.1|BE803572
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG
EST: gi|298174377|gb|HO017713.1|HO017713
EST:     T-GAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAGGGTGATAC
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAGGGTGATAC
EST: gi|6913697|gb|AW395227.1|AW395227
EST:     TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAG                         ATGGAG
genomic: TTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttga ... aatgttgcagATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGACTATTAACGGTGATGATTTGCTCTGGGCCATGGCCACTCTTGGTTTTGAGGATTATATCGATCCTCTTAAAATTTACCTCACTAGATACAGAGAGgtaattttgatttacataatttcacttcttttttaatttcaaaagcttttctggtcccccgaaacaaaattgtctaccgtgtggtttttatttttttagggatttctgctgttggattctgggttttactgatagtattttttttattttttttatttatggctttaccgtggtcgaattgggaatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT