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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgaacaggttttttatgtcatgtcatttctcttgcatttctaaagtactcttacactgtgagcaaagaaagatgttttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG

Basic information

species Glycine max
transcript GLYMA20G32260.1
intron # 9
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G39130.1 (Arabidopsis thaliana), 3'ss of exon 8
------tctttgaacaggttttttat--gtcatgtcatttctcttgcatttcta----aagtactcttacactgtg--agcaaagaaagatgttttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG
            || | ||||| | |     | ||  |   |||||||| |       |||||         |||   | |      | | ||  |  |   | |||    ||  ||||| ||||| ||||| ||||| ||||||||||| |||||||||||||||||||  |||  || |||  ||   ||                      
gtaagtggaccaaatatgttttctttccactacgtattggttcttgcatgttggttggaagtaaaaccgttttgttttaaccgtttcacagGTGGTCAATCCATTTA---CCAAATATGCTTTGACCATATCTCCAGTAGCAATGAGTCTTGAGGAGTTGATACCATCAAGGCATATCAGGTCACATTGGTACG--------------------

upper sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 8
tctttgaacaggttttttatgtcatgtcatttctcttgcatttctaaagtactcttacactgtgagcaaagaaagatgtt-ttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG-----------------------
                         || ||||        | ||  |||     | | | | | | |  | ||   |||    ||| |  |       ||| ||||| |||||  |||| ||||| ||||||||||| |||||||| |||||||||||| |||  |||||   | | ||  | |||  ||| ||||  |                         
-------------------------gtaattt--------tgtcataagcttattcataatataaactgaaaattgtgtggccttaatagaaagaaagcacatatgctttgacattatctccagTTGCAATGAGTCTTGAGGAGTTAATACCATCAAACTATGGGAAGTCACGTTTCTACGCAATCGCCATTAGAAGTGCATTAGCCATCTCTACTCTGCTCGT

upper sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g04660.t01 (Vitis vinifera), 3'ss of exon 10
---tctttgaacaggttttttatgtcatgtcatttctcttgcatttctaaagtactcttacactgtgagcaaagaa-agatgttttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG
        ||  |     |||  |   | |||||| | |    |||      |   |||    |       ||||| |||   ||||| |||||||||   ||| ||||| || || || || ||||| |||||||||||||| |||||||| || ||||||||  |||| ||| |  | ||| | ||| |||| |||||    
cagatgaagagtaaagcatttgagctctttcatttttttctttttttctttttttactttttttaaagaagaagaacagaaaatttttccttaattagagCCACATATGCATTAACCATGTCTCCAGTAGCAATGAGTCTGGAAGAGTTGATCCCTTCAAACCAATCCAAATCTCACATGTATGCAATCCTCATTAGAAC----

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|58019707|gb|CX706449.1|CX706449
EST:     GGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTTTGGAGGAGTTGATACC
genomic: GGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|209702870|gb|BW655992.1|BW655992
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|16104867|gb|BI892607.1|BI892607
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|209702922|gb|BW656019.1|BW656019
EST:     ACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: ACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|105638003|gb|DY577271.1|DY577271
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|9819649|gb|BE555162.1|BE555162
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|14125144|gb|BG789582.1|BG789582
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTGGGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|58017037|gb|CX703779.1|CX703779
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|193410256|gb|FK377167.1|FK377167
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|208151014|gb|GD946047.1|GD946047
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGANACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
EST: gi|15202138|gb|BI425242.1|BI425242
EST:     CTACGGTGGTTAATCCATTTACCAA                         GTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC
genomic: CTACGGTGGTTAATCCATTTACCAAatatccttta ... ttagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtactcttacactgtgagcaaagaaagatgttttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG
                                     ttacttaat  putative branch site 
                          aaagatgttttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgaacaggttttttatgtcatgtcatttctcttgcatttctaaagtactcttacactgtgagcaaagaaagatgttttttacttaattagcttcacGTATGCGTTGACTATATCCCCAGTGGCAATGAGTCTGGAGGAGTTGATACCATCAAACCATGCCAAGTCTTATCTATATTCCATCTTCATCAGAACAGGG

- - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -cttacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa