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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgaactttctgtgattaatattattgtgtttttctgtcatgtgggcttatatccatttttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGGAGATACCACCGAAAGTATAACACTTGGTTTCAGCGGCATGAAGAGCCCA

Basic information

species Glycine max
transcript GLYMA19G28580.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G28580.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------gtac-ctgaactttctgtgattaatattattgtgtt---tttctgtca----tgtgggcttatatccatttt-tttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGGAGATACCACCGAAAGTATAACACTTGGTTTCAGCGGCATGAAGAGCCCA
               | | |||  |  ||| | ||| || || || |      ||   ||||    | | | ||| | | |  | | ||| || ||||  | ||||| |||||| | |||||||| ||| | ||||| ||||| |||||||||||| | ||||  ||||||||||||||| | ||| ||||||| |
gtaccaaaatctcaatgctctgttccatcttttatttatcttcttttccccggttcacgtcaaccttatcgactttttttccctgtgtttgtgtagAACTCATACCAGCAATATCTTGCTGCAAAAGAGCTGAAGAAACAGTCATGGAGATACCACAGGAAGTTCAACACTTGGTTTCAGAGACATAAAGAGCCAA

upper sequence: GLYMA19G28580.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 14
----------------gtacctgaactttct-gtgattaatattattgtgtttttctgtcatgtgggcttatatccatttttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGGAGATACCACCGAAAGTATAACACTTGGTTTCAGCGGCATGAAGAGCCCA
                ||| |    |||  | ||| |||  ||||| ||| || |||      |   || |    ||||  |||||| |||||||||| || ||||||||||||||||| ||  |||||||||| || |||||||||||| | || |||||||| ||||||||| ||||||| ||||| |
gtattgttagctttctgtaacaatccttcatagtgtttaccattat-gtggttatcttgagcatattctcaagcgcattactttctgtagAATACTTATCAGCAATATTTGGCTGCAAAAGAACTAAAGAAGCAATCGTGGAGATACCACAGGAAATATAACACATGGTTTCAGAGGCATGAGGAGCCAA
















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|207828022|gb|GD798837.1|GD798837
EST:     TGATACTCTGTTCTTTGCATTTTATTATCAACAG                         AATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
genomic: TGATACTCTGTTCTTTGCATTTTATTATCAACAGgtacctgaac ... ttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
EST: gi|8402502|gb|BE058136.1|BE058136
EST:     GTTCTTTGCATTTTATTATCAACAG                         AATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
genomic: GTTCTTTGCATTTTATTATCAACAGgtacctgaac ... ttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
EST: gi|22929218|gb|BU546357.1|BU546357
EST:     TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAG                         AATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
genomic: TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAGgtacctgaac ... ttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
EST: gi|27426935|gb|CA938455.1|CA938455
EST:     TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAG                         AATACTTACCCACAA
genomic: TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAGgtacctgaac ... ttttctgcagAATACTTACCAACAA
EST: gi|11687486|gb|BF595162.1|BF595162
EST:     TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTNTATTATCAACAG                         AATACTTACCAACAATATNTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
genomic: TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAGgtacctgaac ... ttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGG
EST: gi|7232311|gb|AW567668.1|AW567668
EST:     TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAG                         AATACTTACCAAC
genomic: TTGAACCATTTGGCACTGATACTCTGTTCTTTGCATTTTATTATCAACAGgtacctgaac ... ttttctgcagAATACTTACCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatattattgtgtttttctgtcatgtgggcttatatccatttttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGGAGATACCACCGAAAGTATAACACTTGGTTTCAGCGGCATGAAGAGCCCA
 gattaat  putative branch site (score: 3)
                                    tatccatttttttct  putative PPT
                                 ttatatccattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgaactttctgtgattaatattattgtgtttttctgtcatgtgggcttatatccatttttttctgcagAATACTTACCAACAATATTTGGCTGCAAAGGAGTTAAAGAAGCAGTCTTGGAGATACCACCGAAAGTATAACACTTGGTTTCAGCGGCATGAAGAGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA