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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagtgagtattgtacatggcatacttatccaccatgtgttgatatttctttgggaatgaattcaacctaacctgttttattcttaatataatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTTAATTTACTTGGTGTCAAGGGTGCCAACAAAGAATCTCCGGGTGCAAATT

Basic information

species Glycine max
transcript GLYMA09G32850.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G32850.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0044g01740.t01 (Vitis vinifera), 3'ss of exon 4
gcagtgagt-attgtacatggcatacttatccaccatgtgttgatatttctttgggaatgaattcaacctaacctgttttattcttaatataatttct--cagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTTAATTTACTTGGTGTCAAGGGTGCCAACAAAGAATCTCCGGGTGCAAATT
   || | | |||    |   ||| | | ||    |||| ||| |  |  |    || | |     |  ||      |  |    |  |||   | |   ||||| ||||| || ||||||||||| ||||| |||||||||||||| || || ||  |||| ||||| |||||||| | |||||| ||||| ||  |||| |
---gtaaatcattagcaacaccatccat-tctgttatgt-ttgcttgtagtagcagactaagaaagaaatattagactaaacatatggtatgggtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT
















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|17022704|gb|BM093738.1|BM093738
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|19346557|gb|BM891437.1|BM891437
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|15814590|gb|BI786865.1|BI786865
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|17023303|gb|BM094337.1|BM094337
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|6566625|gb|AW234266.1|AW234266
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|17023963|gb|BM094997.1|BM094997
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|31457643|gb|CD399671.1|CD399671
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|298168676|gb|HO009606.1|HO009606
EST:     TCAATGGTGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|298174767|gb|HO017876.1|HO017876
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|192318251|gb|FK010991.1|FK010991
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|9819774|gb|BE555287.1|BE555287
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|18692885|gb|BM521733.1|BM521733
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|5057595|gb|AI736071.1|AI736071
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|16347226|gb|BI972821.1|BI972821
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
EST: gi|151397901|gb|EV267774.1|EV267774
EST:     TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAG                         GTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT
genomic: TCAATGATGGCAAGGACCTTCATGTTTCCGTGACCATGCCCTCCATTGAGgtaccactgt ... aatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttgggaatgaattcaacctaacctgttttattcttaatataatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTTAATTTACTTGGTGTCAAGGGTGCCAACAAAGAATCTCCGGGTGCAAATT
                                               tttctc  CT-rich tract
                       taacctgttttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagtgagtattgtacatggcatacttatccaccatgtgttgatatttctttgggaatgaattcaacctaacctgttttattcttaatataatttctcagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTTAATTTACTTGGTGTCAAGGGTGCCAACAAAGAATCTCCGGGTGCAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - gtacatg
- - - - - - - - - -gcatact
- - - - - - - - - - - - - - -ccaccat
- - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaccta