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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactactttattttactcccttattttttaacttctttcttttatttctctagttttaaataactttttttttatttatcatgacaagttctcacgttttaccctcactctactttcaatattttagacattataagtatggaattattaaaagttttaagtttataaataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTTGCTAAAGAACCGATAGACGTGAAACCAGGTGCATGTGGAACCGTTGTAA

Basic information

species Glycine max
transcript GLYMA13G44950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44950.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G51680.3 (Arabidopsis thaliana), 3'ss of exon 1
gtactactttattttactcccttattttttaacttctttcttttatttctctagttttaaataactttttttttatttatcatgacaagttctcacgttttaccctcactctactttcaatattttagacattataagtatggaattattaaaagttttaagtttataaataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTTGCTAAAGAACCGATAGACGTGAAACCAGGTGCATGTGGAACCGTTGTAA
                                                                       | ||  | | || ||||  | | ||     ||  |      |  ||    | || ||   || ||| | |    | | |||    ||||| ||  ||||| | ||  ||||||||||||||| || ||||| || |||||| ||||||| |||| |||||| || |||||  |    || ||  |||| || ||||| || |||||||
----------------------------------------------------------------------atataaatgttat-acaaaatttgaccaaaaacgtttttaagaaatttgccacttcag---ttttaaattttacgtaactaa---ctttaatttattaaatgatta--gGGATACGGAATGACGGAAGCAGGTCCAGTGCTAGCAATGTCGTTAGGTTTTGCAAAGGAACCTTTTCCGGTTAAGTCAGGAGCTTGTGGTACTGTTGTAA
















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|17519294|gb|BM188336.1|BM188336
EST:     ACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: ACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
EST: gi|308222709|gb|HO760619.1|HO760619
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGATTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
EST: gi|308098300|gb|HO760041.1|HO760041
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
EST: gi|11688304|gb|BF595980.1|BF595980
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
EST: gi|4291527|gb|AI437632.1|AI437632
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
EST: gi|16348922|gb|BI974517.1|BI974517
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAG
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAG
EST: gi|21888604|gb|BQ741817.1|BQ741817
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCT
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCT
EST: gi|151407066|gb|EV276881.1|EV276881
EST:     AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: AACTCGAAGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
EST: gi|21677924|gb|BQ630275.1|BQ630275
EST:     AGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAG                         GGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT
genomic: AGACACTCTCAGAGCTAAATTCCCCAACGCCAAACTTGGCCAGgtactacttt ... ataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagacattataagtatggaattattaaaagttttaagtttataaataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTTGCTAAAGAACCGATAGACGTGAAACCAGGTGCATGTGGAACCGTTGTAA
              tatggaattattaaaa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactactttattttactcccttattttttaacttctttcttttatttctctagttttaaataactttttttttatttatcatgacaagttctcacgttttaccctcactctactttcaatattttagacattataagtatggaattattaaaagttttaagtttataaataaatacagGGATACGGAATGACTGAGGCAGGGCCTGTGCTAACAATGTCTTTAGCTTTTGCTAAAGAACCGATAGACGTGAAACCAGGTGCATGTGGAACCGTTGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC