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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttgcttgatcccgtcttactgcttaatcaatcaaaatcaaaacttactttcatgcttctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATTGCTCGTTACG

Basic information

species Glycine max
transcript GLYMA16G00360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G00360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 3
gtacgttttgcttgatc--------ccgtct-tactgcttaatcaatcaaaatcaaaacttactttcatgcttctccttt----cagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATTGCTCGTTACG
||||  |||  || |||         | ||| |  | |||      | |   |   ||  | ||   | | |  |   ||     ||||||| || |||||||| || |||||||| || ||||||||||||||||| || |||||||
gtacagttt-tttaatcaaaggaaatcatctgtggtacttg--tgtttaggtttttaatattctaaaaggatgttatgttgatgtagGTTCCCGTGTTGGAAACACCTGATGGTCCTGTATTTGAGAGCAATGCCATAGCGCGTTACG
















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|192332370|gb|FK026035.1|FK026035
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213607318|gb|DB965148.1|DB965148
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|209699300|gb|BW670264.1|BW670264
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|193451323|gb|FK417883.1|FK417883
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCG
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCG
EST: gi|208282952|gb|GE079818.1|GE079818
EST:     CCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTCGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: CCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213587829|gb|DB959653.1|DB959653
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|192322478|gb|FK014959.1|FK014959
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213615347|gb|DB963541.1|DB963541
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|17023211|gb|BM094245.1|BM094245
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213617072|gb|DB961552.1|DB961552
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|208126057|gb|GD926029.1|GD926029
EST:     CCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: CCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|209714829|gb|BW674315.1|BW674315
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213596059|gb|DB966306.1|DB966306
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCCTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|254343639|gb|GR857395.1|GR857395
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|209706650|gb|BW676159.1|BW676159
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213600558|gb|DB960106.1|DB960106
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
EST: gi|213611109|gb|DB972697.1|DB972697
EST:     GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAG                         GTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT
genomic: GTGTCTCTAATAGAACTCCTGAATTCCTTAAAATGAATCCCATAGGAAAGgtacgttttg ... ctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttactgcttaatcaatcaaaatcaaaacttactttcatgcttctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATTGCTCGTTACG
                            aacttac  putative branch site (score: 2)
                              cttactttcatgcttc  CT-rich tract
          ttaatcaatcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttttgcttgatcccgtcttactgcttaatcaatcaaaatcaaaacttactttcatgcttctcctttcagGTTCCTGTCTTGGAAACGCCCGATGGTCCAGTCTTTGAGAGCAATGCCATTGCTCGTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA