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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

Basic information

species Glycine max
transcript GLYMA02G00580.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatg-cattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                                  |  | |  | ||  |     ||||  | | ||| ||  | | |  |||  |||    || | | |  |||    | ||||    || |||||||| |||||||| || |||||||||||||| ||||| ||||| || || ||||| ||||| || |||   ||||| ||||||
--------------------------------------------------gtaagcatcgtttaca----taaatatctcgtgccatggacctcttgagtttgcagtaaagaaattgaata--atttcaac-tatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG

upper sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                     ||   |   ||           |||   |  |||    |  |    ||||   |   || ||| |    |||   |||   | || |  | ||      |||||||| ||||| || || |||||||||||||||||||||| |||||| ||||||||||| || ||||||   ||||||||||||
-----------------------------------gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcg--ataattttttcgggttttcttcctat------agGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG

upper sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
lower sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                             || | |   ||  |||   ||  |||    |  |||  |        | || |||    | |||  ||     ||     ||      |  |||||||||||||| || || |||||||||||||||||||||| ||| ||||||||||||||||| ||||||   |||||||| |||
--------------------------------------------gtaggtgaagccaacctattcctatttgtggtctttgattt------ctttggtgtaa-ataaata-atatgggtgaataatcttgagatttagGTGGTCTCTTGGCGCCATTATGTATGAAATGCTTGTGGGGTTTCCGCCCTTTTATTCAGATGACCCAATGACAACTTGTAGGAAG

upper sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 6
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                      |  || ||||       |   | ||  | | |   |  | || |  | ||| |||        || ||     ||    ||  ||| | |||   ||||||||||||||||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| |||   |||||||| |||
-----------------------------------gttggttctctaaaa-----ctgtcatcatcttctatgatctgttttccccatggatta-------gtttcctcatataaccat-ctgtttgaatttctccagGTGGTCTCTTGGTGCTATCATGTACGAAATGCTTGTGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG

upper sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                                                                ||   |     |||||||      |   | |   ||    |||  | |  |   | |||||||||||||||||||||||||| || ||||| || |||||||| ||||| ||||| || ||||| ||||  |||||  | |||
--------------------------------------------------------------------------------gtaagaggcatttctgattgaaaatatctaccggcttg-attgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

upper sequence: GLYMA02G00580.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                                                                                ||   |     |||||||      |   | |   ||    |||  | |  |   | |||||||||||||||||||||||||| || ||||| || |||||||| ||||| ||||| || ||||| ||||  |||||  | |||
--------------------------------------------------------------------------------gtaagaggcacttctgattgaaaatatctaccggcttg-attgatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

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|9820829|gb|BE556339.1|BE556339
EST:     ATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG                         GTGGTCTCTTG
genomic: ATTGCTCCAGAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTGgtaatataga ... atgcttccagGTGGTCTCTTG
EST: gi|14009256|gb|BG725860.1|BG725860
EST:     GAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTG                         GTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTT
genomic: GAAGTTCTTCTGAAGAAAGGATATGGCGTGGAATGTGATTGgtaatataga ... atgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG
                             ttctaat  putative branch site (score: 2)
                                              tgcttcc  putative PPT
                            attctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatagaatatgttttctacttttctttttcaaaagtctccctaagggccaccccccttcccccttttaaacttattgtgtcaatgcattctgatgttgtgtcaatgcattctaatgttgtgtcaatgcttccagGTGGTCTCTTGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCACCCTTTTATTCAGATGAACCAATGTTGACTTGTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG