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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCACAAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatagtttgctagtacttactgtatacagttttttctctgaagtctgatcatgtttaatgttgtgtttttgaaaataatag

Basic information

species Glycine max
transcript GLYMA16G33380.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 12
TTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCACAAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgta---agtatagtttgctagtacttact-gtatacagttttttctctgaagtctgatcatgtttaatgttgtgtttttgaaaataatag------------
 ||||||||||||||  |||| |||||||| || ||| |||||||||| |||||||||||  | ||||| ||| |||  |||||    || || ||||| |||   | || | | | || ||    ||| ||  | |  ||     |||  |     |||   | |  |  | |  |     | | || |            
CTATGAAGCTGCTGCTTTAGCATTTGAAGCAATTCCAAGAACTTTGGCTCAAAATTGTGGGTTGAATGTCATCAGGATAATGACACAACTCCAGGGAAAGgtaataattaaactcttcttgttaacacttgtggaaatgttggaagctggggctc--tcagtctcagaggagggactccagcattcatggatcctgtctaga

upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 12
TTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCACAAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtat----agtttgctagtacttactgtatacagttttttctctgaagtc-tgat-catgtttaatgttgtgtttttgaaaataatag---------
 |||||||||||||| ||||| ||||| || || ||| | |||||||| |||||||||||  | ||||| ||  |||  |||||    || || ||||| ||||  ||    |   | ||  ||  |  ||| |  | || |  || ||| |   || | ||||  |  | |        | | ||   | |         
CTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGGGAAAGgtaataatcccaaaactccttttatgt-ttgtgtgaacttgtccctgtgaggaagtggtacatgccttctatcagaagcatcataaacttggcatttaggt

upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 11
TTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCACAAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatagtttgctagtacttactgtatacagttttttctctgaagtctgatcatgtttaatgttgtgttt-ttgaaaataatag-------------
|||||||||||||||  |||||||||| || || ||||| ||||||||||| |||||||| || ||||||||  |||||||||||||| | || ||||| |||||    || |     ||  ||     | |  |||   || |  |||  | |   |  | || |||       |||| ||  |               
TTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTGGCACAGAATTGTGGTGTGAATGTGATTAGGACTATGACTGCTTTGCAGGGAAAGgtaagagctgtatttagttatatatacctttctctttgagcttttgagttcgcttgagagtgattttgcaagggctgaagatgctgtttagtgcctggaa

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|6725259|gb|AW309658.1|AW309658
EST:     AACATTGTGGAGTCAATGTGATCCGGACTATGACTGCTCTACAAGGAACA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
EST: gi|13180864|gb|BG352204.1|BG352204
EST:     AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
EST: gi|6071767|gb|AW101154.1|AW101154
EST:     GGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: GGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
EST: gi|254341468|gb|GR850681.1|GR850681
EST:     AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
EST: gi|192305641|gb|FG998019.1|FG998019
EST:     AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
EST: gi|9440409|gb|BE440914.1|BE440914
EST:     AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
EST: gi|254341467|gb|GR850680.1|GR850680
EST:     AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT
genomic: AAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatag ... aaaataatagCATGCAAATGGAGAAAATGCGTGGATTGGTATAGATGGAAATACTGGTAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCACAAAATTGTGGAGTAAATGTGATCCGGACTATGACTGCTCTACAAGGAAAAgtaagtatagtttgctagtacttactgtatacagttttttctctgaagtctgatcatgtttaatgttgtgtttttgaaaataatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA