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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgctaagcaagttatattttgcatgatatatttgaataataaacgtaacagccatcaaatcttttacgttaattaatgcatcattttctttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAGTGTGTGATATA

Basic information

species Glycine max
transcript GLYMA05G32260.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32260.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g01400.t01 (Vitis vinifera), 3'ss of exon 4
---ctgc-taagcaagttat-attttgcatgatatatttgaataataaacgtaacagccatcaaatcttttacgttaattaatgcatcattttctttgcc-tgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAGTGTGTGATATA
    | | |    |||||   | || |||  |  ||||  ||  ||  |  |       || | |    |||  |||  |  | |   | | ||| || | ||||| | | ||| ||||| || |||||||||||||| ||||||||||| |||||| |||| ||||| ||||||||||||||    | ||    | | |   |  
aacttacatttataagttgccaattagcaaaacctatt--aaagattgatatt----tgattagagtgcttattttatatcttactgaagtctctatgtcatgcagACGAAAGGCCGGGCCCATGATGATGAAGCAATTGAGAAAATGTTGAATGACTTGTCTTTGATCAAGAAATTTGAATAGTAGCCTCTTCATATTTAGAACC
















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|7591146|gb|AW706885.1|AW706885
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|15664606|gb|BI701977.1|BI701977
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAANCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|209729464|gb|BW651831.1|BW651831
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|192323976|gb|FK015697.1|FK015697
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|213604131|gb|DB974229.1|DB974229
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|9899186|gb|BE608084.1|BE608084
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|213591496|gb|DB955760.1|DB955760
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|193692602|gb|FK632803.1|FK632803
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|120533986|gb|EH262119.1|EH262119
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|193487106|gb|FK449301.1|FK449301
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|18718067|gb|BM523023.1|BM523023
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|5509484|gb|AI856042.1|AI856042
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|208043373|gb|GD840091.1|GD840091
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|120534144|gb|EH262277.1|EH262277
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|9898920|gb|BE607888.1|BE607888
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|207688360|gb|GD672181.1|GD672181
EST:     GTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: GTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|5509324|gb|AI855882.1|AI855882
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
EST: gi|192320820|gb|FK013910.1|FK013910
EST:     TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCAGAAACTGTGGAGGAAGCTATTGCTATGGTTCCATCTATCAAGgtaaaaataa ... ttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacagccatcaaatcttttacgttaattaatgcatcattttctttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAGTGTGTGATATA
                          aattaat  putative branch site (score: 3)
                                    tcattttctttgcct  putative PPT
            aaatcttttacgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgctaagcaagttatattttgcatgatatatttgaataataaacgtaacagccatcaaatcttttacgttaattaatgcatcattttctttgcctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCAATCGAGAAAATGTTAAATGACCTGTCGTTGATTAAGAAATTTGAATAAATACGTCAAAGTGTGTGATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- -ctaagca
- - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttaatgc