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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtcttcttattttgtcaaacttcctcattcatttctaatagttttataatttttttttctatcatccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTTGAACTGCCAGGAGGTATCCCAGAATCTTGGCCTAAGTTGCTGCAAGCTC

Basic information

species Glycine max
transcript GLYMA03G33390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33390.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g03360.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gtatttgtcttcttattttgtcaaacttcctcattcatttctaatagt--tttataatttttt--tttctatcatccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTTGAACTGCCAGGAGGTATCCCAGAATCTTGGCCTAAGTTGCTGCAAGCTC
                  | ||||| |  |   | |   | |  ||| | |    |||   ||||   || | | |      ||    | |  | | ||||||   ||||||||||  || ||||| ||| | |||||  || | |||||||| || |||||||| ||||||||||| ||||| ||| |||| |||||||
tgacaaaatgcaattctttctttgtatcatagctattaaagatatccccttgtgcttcatctagtgacttgtgaatcacaaattatctttactcctacagAGTTTACCTGTGGAGGACTTCTACCGCAGTCGGGGGAAGTTGCTAGAGTTTGATCTTCCAGGAGGAATCCCAGAATCCTGGCCAAAGCTGCTTCAAGCTC
















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|23726673|gb|BU761337.1|BU761337
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|254315932|gb|GR825741.1|GR825741
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|23726305|gb|BU761141.1|BU761141
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|16345633|gb|BI971228.1|BI971228
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|254324727|gb|GR834152.1|GR834152
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|16345511|gb|BI971106.1|BI971106
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|6914606|gb|AW396136.1|AW396136
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATATTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|10252826|gb|BE820592.1|BE820592
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|254324726|gb|GR834151.1|GR834151
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGT
EST: gi|209697268|gb|BW675479.1|BW675479
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTT
EST: gi|254315931|gb|GR825740.1|GR825740
EST:     ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAG                         AGTCAGCCTGTGGAGGGATTTTACCGTAG
genomic: ATGATACTGAATCAGTAGTCAAAGAAAGGCTTCGTATATACAATGAAAAGgtatttgtct ... atccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcctcattcatttctaatagttttataatttttttttctatcatccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTTGAACTGCCAGGAGGTATCCCAGAATCTTGGCCTAAGTTGCTGCAAGCTC
              ttctaat  putative branch site (score: 2)
                               tttttttttctatcat  putative PPT
        attcatttctaatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtcttcttattttgtcaaacttcctcattcatttctaatagttttataatttttttttctatcatccttgcagAGTCAGCCTGTGGAGGGATTTTACCGTAGTAGAGGGAAACTGTTGGAGTTTGAACTGCCAGGAGGTATCCCAGAATCTTGGCCTAAGTTGCTGCAAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT