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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttatccctttcttttctcctaacagtctaggcatttcactttactatagtaaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCCAGGAAAAGAGGAAATGCAAATGTTCCATGAGGCTTATGATGTCGTACTT

Basic information

species Glycine max
transcript GLYMA10G06800.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 7
-tcttatccctttcttttctcctaacagtctaggcatt--tcactttactatagtaaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCCAGGAAAAGAGGAAATGCAAATGTTCCATGAGGCTTATGATGTCGTACTT
     |    ||  | || |   |  ||     |   |    |    | | | ||     ||  |         | |    | ||||   || | ||| ||||||| ||||||||||| |||||||| |||||||| ||||||||| ||||| |||| | | ||||| |  | |   | || ||  | || ||||| ||    
actagaaatattcatgttgtgtgagtagaaggtgagatggcaaaaacattcttgttttctttcaatatctgaattctaattttctttttgacctcttaagCAGACTCCAAATCCAGCTTGGTGTGAATATGCCAGCAAGGGCAGAAAAGATTACAGGGATACAGGAAGTAGAGACACTTCACGAAACATACGATGTTGTT---
















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|193711801|gb|FK642202.1|FK642202
EST:     TCGGCTGCTGGGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCGAG                         ACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCC
genomic: TCGGCTGCTGGGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAGgtatggtttc ... tgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCC
EST: gi|21602706|gb|BQ613037.1|BQ613037
EST:     TCGGCTGCTGGGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAG                         ACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCC
genomic: TCGGCTGCTGGGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAGgtatggtttc ... tgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCC
EST: gi|15815638|gb|BI787913.1|BI787913
EST:     TCGGCTGCTGGCGATGAGGAGGTGGATCTACTTCTACCCGGCACAGCAAG                         ACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAA
genomic: TCGGCTGCTGGGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAGgtatggtttc ... tgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagtaaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCCAGGAAAAGAGGAAATGCAAATGTTCCATGAGGCTTATGATGTCGTACTT
      taaatattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttatccctttcttttctcctaacagtctaggcatttcactttactatagtaaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCAGCGAGGGCAGAACAGATTCCAGGAAAAGAGGAAATGCAAATGTTCCATGAGGCTTATGATGTCGTACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - ccctttc
- - - - - - - - - -cctaaca
- - - - - - - - - - - - - - - - gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggctga