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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttttctctttaacttctgatattgttgaatttgcattttcgatattgggtttttcgttggaattgttcttgatggttttgttttcatgtaattgcagACTCCAAAAGGAATTAATGACTCTCATG

Basic information

species Glycine max
transcript GLYMA20G31920.1
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|8285774|gb|BE023333.1|BE023333
EST:     GCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: GCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|9901119|gb|BE610087.1|BE610087
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|37996736|gb|CF808325.1|CF808325
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|298194301|gb|HO040949.1|HO040949
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|6964528|gb|AW433221.1|AW433221
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|21637783|gb|BM107938.1|BM107938
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|298179578|gb|HO028049.1|HO028049
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|298172997|gb|HO019996.1|HO019996
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCACG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
EST: gi|298170339|gb|HO018963.1|HO018963
EST:     CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAG                         ACTCCAAAAGGAATTAATGACTCTCATG
genomic: CAGCCGCTGCCTTCTCCTAACCCCGTCGACACCTCCGCTGTTTCTCAGAGgtgaatgaaa ... gtaattgcagACTCCAAAAGGAATTAATGACTCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgggtttttcgttggaattgttcttgatggttttgttttcatgtaattgcagACTCCAAAAGGAATTAATGACTCTCATG
                        tcttgat  putative branch site (score: 4)
                                 ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttttctctttaacttctgatattgttgaatttgcattttcgatattgggtttttcgttggaattgttcttgatggttttgttttcatgtaattgcagACTCCAAAAGGAATTAATGACTCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA