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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgtggaatgacttatggaggttgagataattgcataatgttattgaatttgtattggttgcaaaaaaaataaactatttattaatgacttgattgtagACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGGAGAGACAGGCCAATTTCAGAGTCATTGAAGCTCTTTGAGGATATGAAAA

Basic information

species Glycine max
transcript GLYMA10G41920.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 12
----aacgtggaatgacttatggaggttgagataattgcataatgttattgaatttgtattggttgcaaaaaaaataaactatttattaatgacttgattgtagACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGGAGAGACAGGCCAATTTCAGAGTCATTGAAGCTCTTTGAGGATATGAAAA
    || |  || |   ||   || |||       |||  |    ||  |||  || |  |      |    | | ||  ||| ||  ||    ||||||| |||||||||| |||||||| ||  ||||||| |||||  |||| ||||||||||| || || |||||   ||| |||||||| || ||||| || |||| | 
aagaaatggtgatttcttttctgatgttagttcttttgttttgcattcatgaggtttttcta----tagttgagaaaagttatctaaaaagtcattgattgcagACACCTGAAGAGATAAAAGAATATAGGGAAAAGAAGATGAATAGTCCTTGGAGGGATAGACCAATCGAAGAATCATTGAAACTGTTTGATGAAATGAGAC
















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|254327577|gb|GR837186.1|GR837186
EST:     AATTAGCAGTGGAGCTCATAAAAAAGGGTCATGCTTATGTTGATCATCAG                         ACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGG
genomic: AATTAGCAGTGGAGCTCATAAAAAAGGGTCATGCTTATGTTGATCATCAGgttggtatct ... ttgattgtagACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGG
EST: gi|298179583|gb|HO028054.1|HO028054
EST:     AATTAACAGTGGAGCTCATAAAAAAGGGTCATGCTTATGTTGATCATCAG                         ACACCTGATGAGCTAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGG
genomic: AATTAGCAGTGGAGCTCATAAAAAAGGGTCATGCTTATGTTGATCATCAGgttggtatct ... ttgattgtagACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttgtattggttgcaaaaaaaataaactatttattaatgacttgattgtagACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGGAGAGACAGGCCAATTTCAGAGTCATTGAAGCTCTTTGAGGATATGAAAA
                  aaaaaaaataaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgtggaatgacttatggaggttgagataattgcataatgttattgaatttgtattggttgcaaaaaaaataaactatttattaatgacttgattgtagACACCTGATGAGATAAAGGAGCATAGGGAGAAGAAATTGAACAGTCCTTGGAGAGACAGGCCAATTTCAGAGTCATTGAAGCTCTTTGAGGATATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT