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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACTCTAAACTGTGAAAAAACCACTGCGATCAATGGCAACGATCAAGGCCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttgctctttcaccatttcctcttgtcgttttctgtttggatactgagaaaatgtgcgagacaaaaaataagttcacgttctattttcggtgtt...

Basic information

species Glycine max
transcript GLYMA09G28100.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28100.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g14450.1 (Oryza sativa), 5'ss of exon 1
AAAACTCTAAACTGTGAAAAAACCACTGCGATCAATGGCAACGATCA---AGGCCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttgctctttcaccatttcctcttgtcgttttctgtttggatactgagaaaatgtgcgagacaaaaaataagttcacgttctattt-tcggtgtt
    | |  | ||  ||   | ||  | |   | |||||  ||| ||   ||  |||||| || ||||||||||||||||||||||| || || |||||||| ||  | |  |            |||    |   |  |   |       | |  |    | |   ||    |      | ||  | ||| ||  |  | |  
---TCCCCGATCTAAGATCCATCCGATCCAGGCCATGGCGGCGACCATCCAGAGCGTGAAGGCCCGCCAGATCTTCGACAGCCGTGGCAACCCCACCGTCGAGgtacgccgcgggtccagtttcgttctgtctagggcgtcgcggcgattgaatcgggtgctttcttagcgcgatgccgcgatcttggtctgttggttagagc-

upper sequence: GLYMA09G28100.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 5'ss of exon 1
AAAACTCTAAACTGTGAAAAAACCACTGCGAT--CAATGGCAACGATCAAGGCCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttgctct--ttcaccatttcctcttgtcgttttctgtttggatactgagaaaatgtgcgagacaaaaaataagttcacgttctattttcggtgtt
  |||    ||   |    | | |   | ||   |||||||||| ||||||| | | |||||||| |||||||||||||||||||||||||| ||||| ||||| ||| |   | |  |||| |  ||       |||   | |  | |  | |    |  || |      |      ||  || |   | |   || | | | 
--AACAAGGAAACCTCGTGAGATCGAAGTGACGACAATGGCAACCATCAAGGTCATCAAAGCTCGACAGATCTTCGACAGCCGTGGAAATCCCACCGTTGAAgtcagtttcattttgtttcagccgtttgatccctcgaaattt-ctcgatttccaccagcattttgatctctgtttttattttaattatttgaatttgctat-
















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|21285613|gb|BQ473484.1|BQ473484
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|209710951|gb|BW656980.1|BW656980
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|7796588|gb|AW781985.1|AW781985
EST:     GTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: GTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|209712453|gb|BW671305.1|BW671305
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|37994573|gb|CF806274.1|CF806274
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|192322987|gb|FK016718.1|FK016718
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|17022623|gb|BM093657.1|BM093657
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|15814140|gb|BI786415.1|BI786415
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|209704369|gb|BW678365.1|BW678365
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|298175490|gb|HO018201.1|HO018201
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|16996515|gb|BM085887.1|BM085887
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|19052750|gb|BM731417.1|BM731417
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|18730045|gb|BM525649.1|BM525649
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|24135517|gb|BU926027.1|BU926027
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|37995932|gb|CF807521.1|CF807521
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|254320851|gb|GR827300.1|GR827300
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|254319290|gb|GR828910.1|GR828910
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
EST: gi|209701948|gb|BW683177.1|BW683177
EST:     CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAA                         GTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC
genomic: CCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttg ... tttatgtcagGTTGACGTTATTCTCAGCGATGGAAGCTTCCACAGAGCCGCCGTGCCTAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAACTCTAAACTGTGAAAAAACCACTGCGATCAATGGCAACGATCAAGGCCGTGAAAGCTCGCCAGATCTTCGACAGCCGTGGAAATCCAACCGTCGAAgtgagtcttgctctttcaccatttcctcttgtcgttttctgtttggatactgagaaaatgtgcgagacaaaaaataagttcacgttctattttcggtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaata