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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcatactttcacttcattcgtatttttttttgtttcatttggtttgcagagaagctgaatcgtgtgttcccatttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG

Basic information

species Glycine max
transcript GLYMA06G15680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G112865_T02 (Zea mays), 3'ss of exon 1
-----------------------------------------------gttagttcatactttc---acttcattcgtatttttttttgtttcatttggtttgcagagaagctgaatcgtgtgttcccatttatct---agAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG
                                                | || ||   ||||     |  ||        | | |    ||  | ||  | ||   |  | |||      ||      | |  |    || || ||||| |||||| |||||||||||||||||||||| || || |||||||||
gtaaattccgcaagcttggccgcgattactcccaacgcatctgcatgctcaggtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG

upper sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
--gttagttcatactttcacttcattcgtatttttttttgtttcat-ttggtttgcagagaagctgaatcgtgtgttcccatttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG
   |   ||  ||          |  | | | |  | ||| |     | |  |||| |   | || | | |  |  || |        || || ||||| |||||| |||||||||||||||||||||| || || |||||||||
gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggc--agGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG

upper sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 1
------gttagttcata---ctttcacttcattcgtatttttttttgtttcatttggtttgcagagaagctgaatcgtgtgttcccattta-----tctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG
       ||   | |||    || ||  || |  || ||       ||      ||  | | || |    | ||   |   | |  ||||      |  ||||| ||||| |||||||||||||||||||||||||| ||||| || |||||||||
gtttcaattcaattataagttttccaaatcttgggtcttaccagccgtacggactgaat-gtagtgtttttaaaattttcttccttattttatgccttcagAACAATGGTGTCGCAGTTGGTGAAGCACGAGCGCATTGAAACCACCGTTGCCAAG

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|298180743|gb|HO022182.1|HO022182
EST:     AAGTTCAGGAAATTGGGTTGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGCCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|298170767|gb|HO015743.1|HO015743
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|192322981|gb|FK016712.1|FK016712
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|192306136|gb|FG993698.1|FG993698
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|151396812|gb|EV266685.1|EV266685
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|192306137|gb|FG993699.1|FG993699
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|192317271|gb|FK010502.1|FK010502
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|298174884|gb|HO014801.1|HO014801
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|151407106|gb|EV276921.1|EV276921
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|151395463|gb|EV265340.1|EV265340
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|192317270|gb|FK010501.1|FK010501
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|192299353|gb|FG990749.1|FG990749
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
EST: gi|7588869|gb|AW704655.1|AW704655
EST:     AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCG                         AACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC
genomic: AAGTTCAGGAAATTGGGTCGACCCACCGGTCACCGAATGTCCATGCTCCGgttagttcat ... atttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtttcatttggtttgcagagaagctgaatcgtgtgttcccatttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG
                                        ttcccattt  CT-rich tract
                                             atttatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcatactttcacttcattcgtatttttttttgtttcatttggtttgcagagaagctgaatcgtgtgttcccatttatctagAACCATGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC