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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggcattcaacttttcccagacataaataactatatattcccatttcaattttgctcttcctttcgccactaacaagcttcatcatcatcctaattttattttgggggcccatcattttatgtttctcaatttaactgtgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTATTGGAGAAGATGGGCCTATTCCTGGGTACTTATGTTGGTGCAAACGCAA

Basic information

species Glycine max
transcript GLYMA13G40190.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40190.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 12
gtatgtggcattcaacttttcccagacataaataactatatattcccatttcaattttgctcttcctttcgccactaacaagcttcatcatcatcctaattttattttgggggcccatcattttatgtttctcaatttaactgtgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTATTGGAGAAGATGGGCCTATTCCTGGGTACTTATGTTGGTGCAAACGCAA
                     ||     | ||   ||  ||| |   | |||| ||||  | |||||||     ||       ||   |  ||  | |   ||  |||            ||||     | |  |  ||  |||||  |||||||||| |    |||||||| ||||  | ||||||  |||||  |||||||||||||||||| ||||| ||||||  ||| || ||||||||||  || ||
-------------------gtccgtctgtgaacctcttcataatt--aattca-ttttttttttcctttttttcct-------tttgcctccaggccagagtttgttt---------ctgtttttcccctgttgaaata-ttgtgtcatgcagACCCAAATGAAAGGATGACGTTGGATGCTGTTGCAAAGCATGCCTGGGTTATTGGAGAAGAAGGGCCAATTCCTCAGTATTTGTGTTGGTGCAGGCGAAA
















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|6719737|gb|AW307384.1|AW307384
EST:     TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
genomic: TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
EST: gi|254333800|gb|GR848718.1|GR848718
EST:     TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
genomic: TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
EST: gi|254333801|gb|GR848719.1|GR848719
EST:     TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
genomic: TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
EST: gi|21256986|gb|BQ453874.1|BQ453874
EST:     TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGANGATGACATTGGGCGATGTT
genomic: TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTT
EST: gi|23058537|gb|BU578321.1|BU578321
EST:     GACATTAACCNNNNNNNNGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
genomic: GACATTAACC-CCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
EST: gi|7639333|gb|AW733658.1|AW733658
EST:     TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
genomic: TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
EST: gi|7684797|gb|AW755445.1|AW755445
EST:     TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAG                         ACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA
genomic: TGACATTAACCCCCAGTTGAAGAATTTAATAGAAGGATTACTATGCAAAGgtatgtggca ... tgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttattttgggggcccatcattttatgtttctcaatttaactgtgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTATTGGAGAAGATGGGCCTATTCCTGGGTACTTATGTTGGTGCAAACGCAA
                     attttatgtttctcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtggcattcaacttttcccagacataaataactatatattcccatttcaattttgctcttcctttcgccactaacaagcttcatcatcatcctaattttattttgggggcccatcattttatgtttctcaatttaactgtgttctgcagACCCAGAACTGAGGATGACATTGGGCGATGTTGCTGAGCATATCTGGGTTATTGGAGAAGATGGGCCTATTCCTGGGTACTTATGTTGGTGCAAACGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG