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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagattcaaataattctttcattcttaatcatactctttgattcatataacgttctaactggttactgcatccaactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC

Basic information

species Glycine max
transcript GLYMA06G46640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G46640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
gtcagattcaaataattctttcattcttaatcatactctttgattcatataacgttctaactggttactgcatccaactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC
|| | |    || | || ||| |    |  |    |  ||  |  | | |||   ||| ||     | ||  |     ||||||||||||||||| || |||   | |||| |||||||||| | |||||| |||| |||||| || ||||| || ||||| ||||| || | |||  | || |
gtaaaaggataagatttgtttaagatctgttttatcaattgtaggcttttaagaatcttac-----attgagtttg--taacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC

upper sequence: GLYMA06G46640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
gtcagattcaaataattcttt-cattcttaatcatactctttgattcatataacgttctaactggttactgcatccaact-----aacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC
       |  | |  |  ||  |||| ||   | |  | |||  | ||  |||     |   |  |||||    | |  |     ||||||||||||||||| | |||   |||||| |||||||||||||  | |||||  |||||||||||||||| || ||||| ||||| || ||||| |||||||
------gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
















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|8404240|gb|BE059874.1|BE059874
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
EST: gi|18040777|gb|BM309071.1|BM309071
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
EST: gi|151397508|gb|EV267381.1|EV267381
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
EST: gi|192299072|gb|FG992848.1|FG992848
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
EST: gi|298172884|gb|HO019868.1|HO019868
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
EST: gi|6072102|gb|AW101421.1|AW101421
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
EST: gi|298176866|gb|HO026873.1|HO026873
EST:     ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAG                         ATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC
genomic: ATAAGACTTATGATGATAACTCTTTGATTAAGACTGCCGATATTGGTCAGgtcagattca ... caactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatactctttgattcatataacgttctaactggttactgcatccaactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC
                         ttctaac  putative branch site (score: 1)
         tttgattcatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagattcaaataattctttcattcttaatcatactctttgattcatataacgttctaactggttactgcatccaactaacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG