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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgcatcacattgcagtgtcaaaagtgtatctgtaccttagttcttattttgtcaaatgtttaatgaagaatatgatcttgatttccttgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGACTGACACCAAGAAAGTTGCCA

Basic information

species Glycine max
transcript GLYMA10G00610.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G00610.3 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 7
gattgcatcacattgcagtgtcaaaagtgtatctgtaccttagttcttattttgtcaaatgtttaatgaagaatatgatcttgatttccttgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGACTGACACCAAGAAAGTTGCCA
  | || |    | |   |     ||  | || |   | | |      |  | || ||    ||  |    | ||     |  |||  |||     |||||||||  |||| ||| ||||||||||||||||||||||||||||||| |||||||| ||||||||| |||| 
tttcgcttttagtagacatagtttaaaagcattttcccttcacgaggaaactcgtgaatgtgttcttttttagtactgcttatattatcttactccccagCAAGTGTTTGTTGAGTTGGCAAATGATCCAAAGCTTGTATATCACTGCGGACTGACGCCAAGAAAGCTGCCG
















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|8403273|gb|BE058907.1|BE058907
EST:     ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAG                         CAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
genomic: ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAGgtgattatta ... tgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
EST: gi|16344608|gb|BI970203.1|BI970203
EST:     TGAAGGGAGCCCTTGCGCCTGCNNAGCAAGAG                         CAAGTCCTGGTGGAGCTGGCAAATGATCCAAAGCTTTGTATATCACTGTGG
genomic: TGAAGGGAGCCCTTGCGCCTGCACAGCAAGAGgtgattatta ... tgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGC-TTGTATATCACTGTGG
EST: gi|26057582|gb|CA800496.1|CA800496
EST:     ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAG                         CAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
genomic: ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAGgtgattatta ... tgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
EST: gi|14008705|gb|BG725309.1|BG725309
EST:     GCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAG                         CAAGTCCTTTTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
genomic: GCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAGgtgattatta ... tgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
EST: gi|21887209|gb|BQ740422.1|BQ740422
EST:     ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAG                         CAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
genomic: ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAGgtgattatta ... tgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
EST: gi|151393880|gb|EV263751.1|EV263751
EST:     ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGTCTGCACAGCAAGAG                         CAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA
genomic: ACTTAATTGCAAAAGCTCTGAAGGGAGCCCTTGCGCCTGCACAGCAAGAGgtgattatta ... tgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattttgtcaaatgtttaatgaagaatatgatcttgatttccttgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGACTGACACCAAGAAAGTTGCCA
                                 tcttgat  putative branch site (score: 4)
                                       tttccttgt  CT-rich tract
                tttaatgaagaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgcatcacattgcagtgtcaaaagtgtatctgtaccttagttcttattttgtcaaatgtttaatgaagaatatgatcttgatttccttgtaatccagCAAGTCCTTGTGGAGCTGGCAAATGATCCAAAGCTTGTATATCACTGTGGACTGACACCAAGAAAGTTGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- ttgcatc
- - - - - cattgca
- - - - - - - - - - - - - - - - ctgtacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaag