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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccaattatgacttttatgatgaataggtttaagtgcaatactgcagtagtccaagttgtattgcttattgtcttatgatagtgtgctcaatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATATATCGAAGAATTTCG

Basic information

species Glycine max
transcript GLYMA19G42150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G42150.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 3
---aaccaattatgacttttatgatgaataggtttaagtgcaatactgcagtagtccaagttgtattgcttattgtcttatgatagtgtgctcaat-gtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATATATCGAAGAATTTCG
     | | | |||   |  | | |    |   ||   |    |  |    |  |  ||   | ||  ||| |||| ||||  |     ||| ||| |  |||||||||||||||||||||||| ||  | || |||||||| |||||| ||||| | || ||||||||
tttttcaagtcatgttctccaagttttccatcctt---tttgtttataattttttttaataggcatccctttttgt-ttattgtgacacgctaaattggttcagGTTTGTACAGAGGTGAGACCCGCTGCTGATGAAGAACTGCCATCTGCATATGTTGAGGAATTTCG
















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|298170466|gb|HO019090.1|HO019090
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|19934424|gb|BQ079454.1|BQ079454
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|27425324|gb|CA936844.1|CA936844
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|9205376|gb|BE331600.1|BE331600
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAGTTGGTGATCATGTTAAACAA                         GTTTGT-CAGA
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGA
EST: gi|6502294|gb|AW203667.1|AW203667
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|27424501|gb|CA936021.1|CA936021
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|10232617|gb|BE801505.1|BE801505
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|192295752|gb|FG992593.1|FG992593
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|151412172|gb|EV281984.1|EV281984
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
EST: gi|208299695|gb|GE097178.1|GE097178
EST:     TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAA                         GTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT
genomic: TTCTTGAACCTAGGACTGCGCAAGTAGCAATTGTTGATCATGTTAAACAAgtaagtcctc ... aatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtagtccaagttgtattgcttattgtcttatgatagtgtgctcaatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATATATCGAAGAATTTCG
                             ttatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaccaattatgacttttatgatgaataggtttaagtgcaatactgcagtagtccaagttgtattgcttattgtcttatgatagtgtgctcaatgtctcagGTTTGTACAGAGGTGAGACCTGCCACAGACGAAGAACTTCCATCTCCATATATCGAAGAATTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - -agtgcaa
- - - - - - - - - - - - - - - - - - - - tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgct