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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtattcactcacatgcacccttttttgttgtgttgtttttggatgatttggtcttagttctgaattattttagtctgtagagtatttaaattgttattctgtgtgtgtgtttattaatagcaataattattaacaagggtgggttattgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAGAGTTCCCAACATGGAGCCGCTTGTCAAAACAAACACATACGAGAGAGGA

Basic information

species Glycine max
transcript GLYMA15G04780.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04780.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g03940.t01 (Vitis vinifera), 3'ss of exon 12
gtatgtattcactcacatgcacccttttttgttgtgttgtttttggatgatttggtcttagttctgaattattttagtctgtagagtatttaaattgttattctgtgtgtgtgtttattaatagcaataattattaacaagggtgggttattgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAGAGTTCCCAACATGGAGCCGCTTGTCAAAACAAACACATACGAGAGAGGA
                                                   ||||| | | ||||  | | |||||  || ||    ||||| | |   |   || ||||| || | ||  ||   ||  ||||  |||         | ||| |||||| ||||| || || |||||||  || | |||||| ||  | ||||| ||||| ||| | ||||||||||| ||||| || ||||||||||| |||||||||
------------------------------------------------tgcttggt-tgacttcttgagtgtttta-cctttatgcaatttagactaacaagttgagtgtg-gtattttgctaa-gatctttat-gaca-------tctcttgttggcagCTACAACCGAGGCTGGTTTTTCCACAGAGAGCACCGGCTGTGGTTCATAAGGGTTGCTAACATGGAGCCACTTGTTAAGACAAACACATATGAGAGAGGA
















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|51342650|gb|CO983616.1|CO983616
EST:     CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|8403614|gb|BE059248.1|BE059248
EST:     CATGCCCAAAGATGAAGCACAACTATATGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|209711367|gb|BW683864.1|BW683864
EST:     TTTTACAGCATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: TTTTACAGCATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|213595685|gb|DB977967.1|DB977967
EST:     CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|22928907|gb|BU546046.1|BU546046
EST:     CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|120529441|gb|EH257575.1|EH257575
EST:     CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|6483197|gb|AW202379.1|AW202379
EST:     CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
EST: gi|207817648|gb|GD792661.1|GD792661
EST:     CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACT                         TTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG
genomic: CATGCCCAAAGATGAAGCACAACTATACGCGGCAAATGAACTgtatgtattc ... ttgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgtgtttattaatagcaataattattaacaagggtgggttattgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAGAGTTCCCAACATGGAGCCGCTTGTCAAAACAAACACATACGAGAGAGGA
                          tattaac  putative branch site (score: 1)
      tgtttattaatagcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtattcactcacatgcacccttttttgttgtgttgtttttggatgatttggtcttagttctgaattattttagtctgtagagtatttaaattgttattctgtgtgtgtgtttattaatagcaataattattaacaagggtgggttattgctggcagTTACAAACGTGGTTGGTTTTATCATAAAGAGCATCGTTTATGGTTTATAAGAGTTCCCAACATGGAGCCGCTTGTCAAAACAAACACATACGAGAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA