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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctacttttttctttccttccttctctctctctctctctctctttttttagggtttcaatctgattcctctgtgcttgttcttgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGGAAGAGGCTGCGTGGGAATTCCTCAAGCCTGAAGTCTTCGCCGCCATTAT

Basic information

species Glycine max
transcript GLYMA20G38630.1
intron # 1
splice site 3'
intron type U2

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|151408856|gb|EV278664.1|EV278664
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCGAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
EST: gi|13481004|gb|BG510347.1|BG510347
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
EST: gi|213598573|gb|DB958157.1|DB958157
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
EST: gi|298169495|gb|HO020855.1|HO020855
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGAATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
EST: gi|213591380|gb|DB959894.1|DB959894
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
EST: gi|192327952|gb|FK021699.1|FK021699
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
EST: gi|298199497|gb|HO042860.1|HO042860
EST:     TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACG                         GCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG
genomic: TCGTTCTGCAATGAACTCTCCCCTCGCCAAATCGCTCTTCGCAATCGACGgtctctactt ... tgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctttttttagggtttcaatctgattcctctgtgcttgttcttgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGGAAGAGGCTGCGTGGGAATTCCTCAAGCCTGAAGTCTTCGCCGCCATTAT
                     atctgat  putative branch site (score: 4)
                                     cttgttctt  putative PPT
     ttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctacttttttctttccttccttctctctctctctctctctctttttttagggtttcaatctgattcctctgtgcttgttcttgttgtgcagGCGTTACTCGCGTTTTCTTTGGATCTGATTTCGTTACCGTTACGAAATCGGAAGAGGCTGCGTGGGAATTCCTCAAGCCTGAAGTCTTCGCCGCCATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG