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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCAAAATTTTGCTAAAATGTTTGAGATAAACTTTGAAAATGAAAAGGGAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagctttaatttcttgaatatacattcattggaggattcctctacatcatattgcatctatatttgttttttttaacag

Basic information

species Glycine max
transcript GLYMA19G40930.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G40930.4 (Glycine max), 5'ss of exon 9
lower sequence: AT3G62120.2 (Arabidopsis thaliana), 5'ss of exon 8
GGGCCAAAATTTTGCTAAAATGTTTGAGATAAACTTTGAAAATGAAAAGGGAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttt---aatttcttgaatatacattcattggaggattcctctacatcatattgcatctatatttgttttttttaacag
||| ||||| ||||| || ||||||||||| |||||||| ||||| || | ||||| || |||||| ||||||||||| |||||||| |||||  | || ||||    |   || | |||  || ||  ||  |        | ||||||| |   |  | | |   |||      ||| | ||
GGGACAAAACTTTGCGAAGATGTTTGAGATCAACTTTGAGAATGAGAAAGCAGAGACAGAAATGGTGTGGCAGAATTCTTGGGCCTACAGTACCAGGACGgtaaatacttggaagtacttagat-tatttttctcatg----tgctctacaactgttaacttatcattttcaaaccttttatag

upper sequence: GLYMA19G40930.4 (Glycine max), 5'ss of exon 9
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 5'ss of exon 9
GGGCCAAAATTTTGCTAAAATGTTTGAGATAAACTTTGAAAATGAAAAGGGAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagctttaatttc-ttgaatatacattcattggaggattcctctacatcat--attgcatctatat----------ttgttttttttaacag--------
 || ||||||||||| ||||||||||| |||| |||||||||||| |||||||| || || ||||||||||||||||| |||||||| |||||  |||| ||||   | |||  | ||   | |   |   ||| |   |||   |  | ||   |||   | |  |           |  ||||  |  |  |        
AGGTCAAAATTTTGCAAAAATGTTTGATATAACCTTTGAAAATGAGAAGGGAGAAAAGGCTATGGTCTGGCAGAATTCCTGGGCCTACAGTACCAGAACGgtaaa--taaatgacattttttttgtttgagttgaaaagttctaatttaacagcaattatgtttccaaaagggggggataattttcatgcatgggatttctt
















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|193725712|gb|FK657668.1|FK657668
EST:     TATAGTACTCGAACT                         ATTGGGGTCGATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACC
genomic: TATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTC-ATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACC
EST: gi|207831009|gb|GD805067.1|GD805067
EST:     GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
EST: gi|208199816|gb|GD998559.1|GD998559
EST:     GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAAGGGATTGGTACTACC
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAA-GGGATTGGTACTACC
EST: gi|208174450|gb|GD968159.1|GD968159
EST:     GAGAGAAAGCGATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGG
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGG
EST: gi|207734424|gb|GD713312.1|GD713312
EST:     GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGT-CTACCT
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
EST: gi|58014455|gb|CX701197.1|CX701197
EST:     GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCNTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
EST: gi|208320376|gb|GE122097.1|GE122097
EST:     GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
EST: gi|207783076|gb|GD751077.1|GD751077
EST:     GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACT                         ATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT
genomic: GAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagcttta ... tttttaacagATTGGGGTCATGGTGATGGTTCATGGTGATGACAAGGGATTGGTACTACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCCAAAATTTTGCTAAAATGTTTGAGATAAACTTTGAAAATGAAAAGGGAGAGAAAGCAATGGTCTGGCAGAATTCATGGGCCTATAGTACTCGAACTgtaagctttaatttcttgaatatacattcattggaggattcctctacatcatattgcatctatatttgttttttttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA