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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGGTGTTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatttgtaaccccgctctttgatattttcgtttttttcatgttagttttattttctctatgtccatgttgttggttacttacagtttgcttcattttgtag

Basic information

species Glycine max
transcript GLYMA10G28530.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28530.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 2
---GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGGTGTTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaa---------tttgtaaccccgctctttgatattttcgtttttttcatgttagttttattttctctat----gtccatgt-tgttggttacttacagtt-tgcttcattttgtag
    ||||| || || |||||||||||| | ||||| ||    || |   |||||||||| |||||||| |||||||| || ||||||||||||||||| | ||||||| |          |  |    | | |  ||  | ||   |||  ||   | ||   |  | ||  |  ||    |  ||| |   ||||||||| |      | ||| |||||  ||
CATAGCACCTACCTCTGGTTTGAGAGAACCTAGTGGCCACAATGCCG---GTGTTGATAGGTTGCCAGAAGAGATGAATGACATGAAAATTAGGGATGACAAAgtatgtgagggactggtctaatgcttctgtttcttcgtgttactgttccttgtcttttgcctgcacttaattgattattgatcatttgcattggttactgaagacagttcttgatttttcag
















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|5676842|gb|AI937972.1|AI937972
EST:     TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
genomic: TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
EST: gi|298194802|gb|HO043274.1|HO043274
EST:     TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGGCATATC
genomic: TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
EST: gi|254344095|gb|GR851005.1|GR851005
EST:     TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
genomic: TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
EST: gi|21602288|gb|BQ612619.1|BQ612619
EST:     TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
genomic: TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
EST: gi|208184951|gb|GD984951.1|GD984951
EST:     TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGGCAGGACATATC
genomic: TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
EST: gi|7925613|gb|AW831639.1|AW831639
EST:     TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTACGGATGATAGA                         GAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC
genomic: TTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatt ... cattttgtagGAAATGGAAGCCACAGTTGTTGATGGCAATGGAACGGAGACAGGACATATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACCAACTTCGGGTTTGAGAGAAGCCAGTGGGCATGGAGCAGCAGGTGTTGATAGATTGCCAGAGGAGATGAACGATATGAAAATTAGGGATGATAGAgtatgtaatttgtaaccccgctctttgatattttcgtttttttcatgttagttttattttctctatgtccatgttgttggttacttacagtttgcttcattttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG