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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatccattcaattctcaacttagggttattcttccgttttctttttgtctcag

Basic information

species Glycine max
transcript GLYMA10G44070.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 1
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatcc-attcaattctcaacttagggttattcttccgttttctttttgtctcag-
|    |  | |  |||||||| ||| || |||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||||||||||| |||| | ||||| |  | || |     ||| |||   |  || |||||| |    |  ||   | || | ||||  || | |   ||      |     |  |    
GGCGGAAGGGGGGATGGACGACTACGCGCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATCAGGgtacaaatcccccatccctcttcttctcttctcttgctcacctttctgcggatctgactcactacttgcggatctcaatctccggcccgccggaattgct

upper sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G099980_T03 (Zea mays), 5'ss of exon 1
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctc-ttcccaattcctcaccgtagatcca---ttcaattctcaactta-gggttattcttccgttttctttttgtctcag
     |    |  |||||||| ||| |  |||| |||||||| || ||||| || ||||| ||||| ||||||||||| ||||||||||||| |||  | || | |||   |       |||| || || ||     | |  | | |||||        |  | |  || | || |    |||    |  | |   || |   
ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtacttccaacttattttcttcgtttccgccatcccttcattgatccggtgcctcacccacgcctcacggatctagcttttcatcccctccagttt---

upper sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatccatt---caattctcaacttagggttattcttccgttttctttttgtctcag
       |  |  |||||||| ||| |  |||| |||||||| |||||||| || ||||| ||||| ||||||||||| ||||| ||||||| |||  | || | |||  |||      || | || |  | |   | |  | | |||||  |     |  | || |  ||| |    |||       | |   || |   
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg-

upper sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
lower sequence: AT3G55000.1 (Arabidopsis thaliana), 5'ss of exon 1
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacacc------ttagggtttcctcttccca---attcctcaccgtagatccattcaa-----ttctcaacttagggt---tattcttccgttttctttttgtctcag------------------------------------------------------------------------------
     |    |  ||||||||||| || || || |||||||| || |||||  |||||||||| || || ||||||||||| |||||||| | |||||| ||| || | | |        ||   |    | ||| ||   |||  | |  | | ||     ||      |  |    ||    |   ||   | |  ||||  |   ||  | |                                                                              
ATTTGATTTTGTGATGGACGATTATACAAGAGAGATGATGGATCTCAAGACTTTGGTCACTCGAACCCTAGAGAAGAAAGGTGTCCTCGCTAAGATCCGGgtaaattccctctacttctctaccatacattattcgcagaaatttttgagtggaaatgagaacagagaagtgattcgtttgaaatacatacattactctttttctagggttcctgctattcagatcgaaatgctcgatattgttaattgcctatgcatctggaatcttgctgatagtttatttgtgtttgtag

upper sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatccattcaattctcaacttagggttattcttccgttttctttttgtctcag----
         ||| |||||||| |||||  | || ||||||||||| ||||| || |||||||| || || |||||||||||||||||||||| |||||| |||  | |    | |    || ||||||     ||| |   | |    |  |||    |   |  | ||  | || || |   || |   |     |     
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgtattttcctttccttt--ttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgtttcaaattttcaatacgagaaacga

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|298172736|gb|HO019776.1|HO019776
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|17020875|gb|BM091909.1|BM091909
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|7924311|gb|AW830337.1|AW830337
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|15663792|gb|BI701163.1|BI701163
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|298169346|gb|HO020706.1|HO020706
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|151396981|gb|EV266854.1|EV266854
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|298165818|gb|HO008789.1|HO008789
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGATGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|151401442|gb|EV271256.1|EV271256
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|208297408|gb|GE094443.1|GE094443
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|15663781|gb|BI701152.1|BI701152
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|298181217|gb|HO022656.1|HO022656
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|192305408|gb|FG998276.1|FG998276
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GTCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|19937108|gb|BQ081151.1|BQ081151
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCTATGTTATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|4396047|gb|AI495044.1|AI495044
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|298190579|gb|HO032700.1|HO032700
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAGGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|298198081|gb|HO039620.1|HO039620
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|208307294|gb|GE108792.1|GE108792
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|193610993|gb|FK562987.1|FK562987
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
EST: gi|298191405|gb|HO038884.1|HO038884
EST:     CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGT                         GCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG
genomic: CACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacac ... tttgtctcagGCCGAACTCAGGGCGAGTGTGTTCGAAGCCATCGAAGAGGAAGATCGTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatccattcaattctcaacttagggttattcttccgttttctttttgtctcag

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