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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttaaacttgatatcgaattgtctctctgttgaattcacatatttgtgatattgctgacgtttagctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTTTATGATGATGTACCAGAAGCTCTAGAAAAGTGGCACGCCTTGGGTATAA

Basic information

species Glycine max
transcript GLYMA13G35120.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G35120.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 8
gtagttaaacttgatatcgaattgtctctctgttg-aattcacatatttgtgatattgctgacgtttagctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTTTATGATGATGTACCAGAAGCTCTAGAAAAGTGGCACGCCTTGGGTATAA
|||   ||| | ||    ||    | |      ||  |  || |    || ||    ||| || |||    | |||||||||||| |||  |||||| | | |||||||||||||||||||| | |||| ||| ||||| |||||||||||  | |||||||| || |  || ||||
gtaagaaaaatggaatgagagaaatatgatcactgtgaggcagacccctg-gagtcagctaacatttttgcacgcagGGTCATATTTGGCGAACTGGATTTCAGAATAATGAATTGGAGGGAGTCGTTTTTGAGGATGTGCCAGAAGCTCTTCAGAAGTGGCATGCTTCAGGAATAA
















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|22927886|gb|BU545025.1|BU545025
EST:     GCTATGATTAAAGCTGATAGAAAGATCACTGNCTTAAAAGAGTTGCAG                         GGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
genomic: GCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAGgtagttaaac ... agctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
EST: gi|10232167|gb|BE801055.1|BE801055
EST:     TGCCTTAAAAGAGTTGCAG                         GGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
genomic: TGCCTTAAAAGAGTTGCAGgtagttaaac ... agctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
EST: gi|14011393|gb|BG726307.1|BG726307
EST:     ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAG                         GGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
genomic: ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAGgtagttaaac ... agctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
EST: gi|5770700|gb|AI973874.1|AI973874
EST:     ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAG                         GGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
genomic: ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAGgtagttaaac ... agctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
EST: gi|207848425|gb|GD819800.1|GD819800
EST:     ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAG                         GGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
genomic: ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAGgtagttaaac ... agctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
EST: gi|208305995|gb|GE105740.1|GE105740
EST:     ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAG                         GGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT
genomic: ATGCTATGATTAAAGCTGATAGAAAGATCACTGCCTTAAAAGAGTTGCAGgtagttaaac ... agctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctctctgttgaattcacatatttgtgatattgctgacgtttagctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTTTATGATGATGTACCAGAAGCTCTAGAAAAGTGGCACGCCTTGGGTATAA
                                  tgctgac  putative branch site (score: 2)
                     atatttgtgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttaaacttgatatcgaattgtctctctgttgaattcacatatttgtgatattgctgacgtttagctatgcagGGTCATATATGGAAAACTGGCTATGAGAATAATGAATTGGAGGGAATAGTTTATGATGATGTACCAGAAGCTCTAGAAAAGTGGCACGCCTTGGGTATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC