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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttttttgttagatctgattcttgttagtccatttaacagccctgcaaaatgtgttatttttcagctaaatatgtgacctttttttgaacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA

Basic information

species Glycine max
transcript GLYMA13G38040.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38040.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0134g00160.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------------------------------ctttttttttgttagatctgattcttgttagtcca----tttaacagccctgcaaaatgtgttatttttcagctaaatatgtgacctttttttgaacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA
                                                                      | || |  |||  || |  ||||  | | ||      ||| |||    | ||  || |||  |   | |  |   | | | |    |  | ||  | | |||| ||||| |||   || || ||||| || |||||||| || || |  || ||| ||||||| |||||||| ||||||||||| |||||||||||||||||
gtaccataccttcaccaaaatcttcccttttaatcctttttttttttttttttcatatatgaccaatgtgtcttctgggttccatttttttctcatgaatcagctgtttttacattgtttcagtatctgt-gtgactgaagtttgtgtattaatggtgatcgatgatttcagGAGCTGGGTTTTCCTCCAAAAGCAAGTACATGTTTGGAAAGGTCAGTATTCAGATCAAGCTCGTGGAGGGCGACTCTGCTGGGACTGTCACTGCTTTCTA
















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|23730922|gb|BU763570.1|BU763570
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|20076055|gb|BQ094847.1|BQ094847
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|209722326|gb|BW665823.1|BW665823
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCCAACAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|192330868|gb|FK021627.1|FK021627
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|298191789|gb|HO035871.1|HO035871
EST:     TTTCATCCGTGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|254327781|gb|GR834746.1|GR834746
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|33387513|gb|CA850720.1|CA850720
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|19935068|gb|BQ080098.1|BQ080098
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|7284113|gb|AW596712.1|AW596712
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|26056322|gb|CA799236.1|CA799236
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
EST: gi|22525223|gb|BU084034.1|BU084034
EST:     TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTTCTCAAACTCAAACTTGATAACTATTCTGgtaattgatc ... aacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcaaaatgtgttatttttcagctaaatatgtgacctttttttgaacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA
                     agctaaa  putative branch site (score: 3)
     aaatgtgttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttttttgttagatctgattcttgttagtccatttaacagccctgcaaaatgtgttatttttcagctaaatatgtgacctttttttgaacactgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - -ctgattc
- - - - - - - - - - - - - - - - ccattta
- - - - - - - - - - - - - - - - - - - - - -ccctgca