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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttattttacatattatatcatttctatggggactcgtgcgtttatctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG

Basic information

species Glycine max
transcript GLYMA01G37420.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G18100.1 (Arabidopsis thaliana), 3'ss of exon 11
ggttattttacatattatatcatttctatggggactcgtgcgtttatctgttaaataagatgttccctt-attctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
                     ||||||      ||||     ||||||| |    ||  ||   |  || ||||| |  |    |   | |||   || ||||||| | || || ||||||||||||||||||||||| ||| |||||||| | |||||||||  ||  |  ||||||
-------------------gtatttctcc----actca-atatttatctttgctttagaattgacaattgattcttgtctttaacacatttttcacggtagCTGAAATTGTGGAAAGAGTTGTTCTTCTTGGAGCACCAATTTCAATCAAGAATGAGAATTGGCGAGACGTAAGAAAG

upper sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 11
lower sequence: AT4G36210.1 (Arabidopsis thaliana), 3'ss of exon 10
ggttattttacatattatatcatttctatggggactcgtgcgtttatctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
                   | ||||| |  | |     |       |   |||||  |     ||  |  | | | |   ||     ||| | |||| ||||||||| || |||||||||||||||||||||||||||||| |||||||    || || |||  ||  |  || |||
------------------gtaatttccaatgtgcaagatagaagattgctttaaaagatcaaatctttcttacggagactcttaacatgtct-ttggtagCTGAACTTGTGGAGAGAGTTGTTCTTCTTGGAGCACCCATTTCAATCAATAGTGAAAACTGGCGAGACGTAAGGAAG

upper sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv04s0023g02940.t01 (Vitis vinifera), 3'ss of exon 11
ggttattttacatattatatcatttctatggggactcgtgcgtt-tatctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
                           |  || || |    | | | | || |  ||    |||       |  ||  ||| | |     ||  || ||||||||||| || || ||||||||||||||||||||||||||| |  |||  || ||||| ||||||| ||||||||| 
------------------------gtaactggtaccctcaagctgtttgtgatggatggtttgtattgcattaatgatgtgatacacaaatt--tttgcagCTGAACTTGTTGAAAGAGTTGTTCTTCTTGGAGCACCCATTTCGTTCAGAGATGAGAACTGGGAAGTTGCTAGAAAA

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|15201810|gb|BI425071.1|BI425071
EST:     TAGAGTTATTTTCAAGTGTCTGGAGTTTTTGGCTGAAACAGAAAACAGTG                         CTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGG
genomic: TAGAGTTATTTTCAAGTGTCTGGAGTTTTTGGCTGAAACAGAAAACAGTGgtatgtattt ... ttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGG
EST: gi|15202089|gb|BI425216.1|BI425216
EST:     TAGAGTTATTTTCAAGTGTCTGGAGTTTTTGGCTGAAACAGAAAACAGTG                         CTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGG
genomic: TAGAGTTATTTTCAAGTGTCTGGAGTTTTTGGCTGAAACAGAAAACAGTGgtatgtattt ... ttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGG
EST: gi|12773115|gb|BG238042.1|BG238042
EST:     TAGAGTTATTTTCAAGTGTCTGGAGTTTTTGGCTGAAACAGAAAACAGTG                         CTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGG
genomic: TAGAGTTATTTTCAAGTGTCTGGAGTTTTTGGCTGAAACAGAAAACAGTGgtatgtattt ... ttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG
                                      cttctgttt  CT-rich tract
     ttaaataagatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttattttacatattatatcatttctatggggactcgtgcgtttatctgttaaataagatgttcccttattctggggtgctgcttctgtttattggcagCTGAACTGGTAGAGAGAGTTGTTCTTCTTGGAGCACCCATTGCAATCAAGGACGAGAATTGGGAAGCTGCTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - tatgggg
- - - - - - - - - - - - - - - - - ctcgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcttc