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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctgttaaaattgtattccattatgaaatttggtataacagttctgcaatgcttttagtgtgcgatttcttgtctctgttcagtatgtcatgcaatggtggaaaataagcctgttactatacttccttcatgctctcatcatttaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG

Basic information

species Glycine max
transcript GLYMA20G38770.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 14
gtttgctgttaaaattgtattccattatgaaatttggtataacagttctgcaatgcttttagtgtgcgatttc-ttgtctctgttcagtatgtcatgcaatggtggaaaataagcctgttactatacttcct--tcatgctctcatcatttaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG
                                                               ||  || |||   |     | | | | | |   |      |      |    ||||  |  |  || ||  |  | || |  ||  |||  | |   ||  |||| || |||||||||||||| ||||||||||| |||||||| |  |||||||||   || |  || || ||| |||| ||||| |||   |||||| |||
---------------------------------------------------------------gttagacttcaccgatatagatgaatttcttccgtttccttcagttttggatctgtcgcgttgatttctaattctcctgttttcgcttatatctcctctacagGTTGTGGAACTTGATTTTCTGTATCCAAGTGAAGGCATCCACAGGCGTTGGGATGGTGGATTCAGAATCACATCAACAGCAGCCACAACCGATCAAGCTG

upper sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 14
gtttgctgttaaaattgtattccattatgaaatttggtataacagttctgcaatgcttttagtgtgcgatttcttgtctctgttcagtatgtcatgcaatggtggaaaa--taagcctgttactatacttccttcatgctctcatcatttaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG
                                                              |||   ||   ||  || || |     |    |  ||||||   | |  |  |  | | | | |   || |||     ||  ||| | || ||       ||||| || || |||||||||||||||||||||||||||||||| | | | ||||| |  |||||| | || ||| |||| || || || | |||||||||||
------------------------------------------------------------tctgttttatcatttaactatggttgcagttcattataatggttttagagttttggttttgattgtttctctttctctaacttgtcaatgacgttc-----atagGTTGTGGAGCTTGATTTTCTCTATCCAAGTGAGGGCATCCACAGAAGGTGGGACAGTGGTTATCGAATAACATCAACGGCTGCAACTTGGGATCAATCTG
















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|163927003|gb|EH039353.1|EH039353
EST:     GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAG                         GTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
genomic: GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAGgtttgctgtt ... ttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
EST: gi|207754195|gb|GD725193.1|GD725193
EST:     GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAG                         GTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
genomic: GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAGgtttgctgtt ... ttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
EST: gi|254339336|gb|GR848053.1|GR848053
EST:     GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAG                         GTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
genomic: GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAGgtttgctgtt ... ttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
EST: gi|120534539|gb|EH262672.1|EH262672
EST:     GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAG                         GTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG
genomic: GAAGTCGCTGGGGTGTTGTTATGTCTCGAAATGCTGGATTCAGTAAACAGgtttgctgtt ... ttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagcctgttactatacttccttcatgctctcatcatttaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG
                                           ttttaac  putative branch site (score: 2)
                                     tttacctttt  CT-rich tract
         ttactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctgttaaaattgtattccattatgaaatttggtataacagttctgcaatgcttttagtgtgcgatttcttgtctctgttcagtatgtcatgcaatggtggaaaataagcctgttactatacttccttcatgctctcatcatttaccttttaactgtagGTGGTTGAACTTGATTTTCTCTATCCAAGTGAGGGCATCCATAAACGTTGGGATAAAGGTTATAGGATTACAGCAACCGCAGCTACATTGGATCAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT