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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaccaataaaaaaaccgtgtaaaattaaatattgatgtacattgcttatatgggtataagttggaccgttgtcgcttaccctttggtctgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCCAAATTCAGAGCCCCAGTGGAACCCTATTGATTGTTTAGCCCAAGATCAT

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 3'ss of exon 16
-------aggaccaataaaaaaaccgtgtaaaattaaatattgatgtacattgcttatatgggtataagttggaccgttgtcgcttaccctttggtctgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCCAAATTCAGAGCCCCAGTGGAACCCTATTGATTGTTTAGCCCAAGATCAT
            |  |||  || || || | |      |  | | |    |   | | | |||   || ||       |    | | |  |||  | | |    |||||||| |||||||||||||| || ||| | || |||||||| ||||||||||| ||| | || || ||||| ||||| | |   |   |   ||||    
tttttgttcaggcgttaacgaatccatgcata------tgcttaagctagtcattaaaaaggggtaaaattattatactaattcatgctatttcttattt-caacagCTTCTTAGGATTGAGGAGGAGCTTGGTGCGGCTGCTGTCTACGCTGGTGCCAAGTTCCGCGCACCCGTGGAGCCCTACTAAACTTGATGGTGAAGACAGG
















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|58014968|gb|CX701710.1|CX701710
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254343119|gb|GR859281.1|GR859281
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|9258535|gb|BE346682.1|BE346682
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|57574275|gb|CX547250.1|CX547250
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254320423|gb|GR826872.1|GR826872
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254335782|gb|GR847310.1|GR847310
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|10254318|gb|BE822084.1|BE822084
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254341113|gb|GR854841.1|GR854841
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|16343634|gb|BI969229.1|BI969229
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|7588392|gb|AW704189.1|AW704189
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254329397|gb|GR838950.1|GR838950
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|58020394|gb|CX707136.1|CX707136
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTTTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTTTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|213597412|gb|DB977775.1|DB977775
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCAGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|151408704|gb|EV278512.1|EV278512
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254317871|gb|GR832039.1|GR832039
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|17963567|gb|BM270314.1|BM270314
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
EST: gi|254329396|gb|GR838949.1|GR838949
EST:     TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG                         CTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC
genomic: TCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAGgtaaaaatcg ... tgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttatatgggtataagttggaccgttgtcgcttaccctttggtctgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCCAAATTCAGAGCCCCAGTGGAACCCTATTGATTGTTTAGCCCAAGATCAT
                             cgcttac  putative branch site (score: 3)
           tataagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaccaataaaaaaaccgtgtaaaattaaatattgatgtacattgcttatatgggtataagttggaccgttgtcgcttaccctttggtctgtgttgcagCTTCTGAGGATTGAGGAGGAACTGGGTTCTGCGGCTGTCTATGCTGGTGCCAAATTCAGAGCCCCAGTGGAACCCTATTGATTGTTTAGCCCAAGATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - -aaaaaaa
- - - - - - - - - - - -aaattaaa
- - - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - tgcttat