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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatatgatttgaacttggcattcctgttttactagcagtttctgagattagttgttctattcctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGATGCACTGAATAAAGTTCTGCC

Basic information

species Glycine max
transcript GLYMA13G20780.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 8
---gttagatatgatttgaacttggcattcctgttttact-agcagtttctgagattagttgttctattcct--------gtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGATGCACTGAATAAAGTTCTGCC
    ||   | | | |   | |   |     ||||||  | |  || |||||  |     ||| |  |  ||         | ||||| |||||||||||||||||||||| ||||| |||||||| ||||||||||||  || | | |||| ||| ||
gtaattctttttaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattatcttctcattcatgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 8
---gttagatatgatttgaacttggcattcctgttttact-agcagtttctgagattagttgttc--tattcctgtat------gcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGATGCACTGAATAAAGTTCTGCC
    ||   |   | |   | |   |     ||||||  | |  || |||||  |     ||| |  ||||     ||      |||| |||||||||||||||||||||| ||||| |||||||| ||||||||||||  || | | |||| ||| ||
gtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGATCAACAGGAGAAAGCTCTACC
















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|10845490|gb|BF071116.1|BF071116
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|17518725|gb|BM187767.1|BM187767
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|192324906|gb|FK016092.1|FK016092
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|5688475|gb|AI941490.1|AI941490
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|9440259|gb|BE440768.1|BE440768
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|151405346|gb|EV275160.1|EV275160
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAGATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|209697661|gb|BW655508.1|BW655508
EST:     TAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: TAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|151404672|gb|EV274486.1|EV274486
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|9902652|gb|BE611559.1|BE611559
EST:     ATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: ATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|151405163|gb|EV274977.1|EV274977
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGGTGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|10232664|gb|BE801552.1|BE801552
EST:     ATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: ATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|12773014|gb|BG237941.1|BG237941
EST:     CTGCTGATTCCATACAATTAGTTGCTGGACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCC
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCC
EST: gi|21602656|gb|BQ612987.1|BQ612987
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|15287897|gb|BI471788.1|BI471788
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|308098710|gb|HO760451.1|HO760451
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
EST: gi|15199748|gb|BI423990.1|BI423990
EST:     CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAG                         TTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT
genomic: CTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatg ... ctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattcctgttttactagcagtttctgagattagttgttctattcctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGATGCACTGAATAAAGTTCTGCC
                                     ttctattcct  CT-rich tract
         ttttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatatgatttgaacttggcattcctgttttactagcagtttctgagattagttgttctattcctgtatgcagTTCTTCATGATGAACCTTTCTGCCCCATTTATCTGTGAGTTCTTCAAGGATGCACTGAATAAAGTTCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG