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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaaccattttctggtttctttgaagacctgtttagtaatgttattgttaacagaccattatctaattttagacaacatttttttttgttagatctggttcttaacggtccatttaataccattgcaacaaatcatttgtgtgttattttaagctaaacatgttacctttttgggacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCCTGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA

Basic information

species Glycine max
transcript GLYMA12G32390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G32390.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0134g00160.t01 (Vitis vinifera), 3'ss of exon 1
gtaattaaccattttctgg---tttctttgaagacctgtttagtaatgttattgttaacagaccattatctaattttagacaacatttttttttgttagatctggttcttaacggtccatttaataccattgcaacaaatcatttgtgtgttattttaagctaaacatgttacctttttgggacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCCTGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA
|||    ||| |   |      || | ||  |  ||| |||  |  | || ||  ||   ||||| | | |  || | |    ||||||||| |  |  ||| | |  ||     |   || | || |  ||  ||  |   ||||||| ||| |    | | | |              |   ||| |||| ||||| |||   || || ||||| || ||||||||||| || |  || | | ||||||| |||||||| ||||||||||| |||||||||||||||||
gtaccataccttcaccaaaatcttcccttttaatcctttttttttttttttttcatatatgaccaatgtgtc-ttctgggttccatttttttctcatgaatcagctgtttttacattgtttcagtatctgtgtgactgaa-gtttgtgtattaat----ggtgatc--------------gatgatttcagGAGCTGGGTTTTCCTCCAAAAGCAAGTACATGTTTGGAAAGGTCAGTATTCAGATCAAGCTCGTGGAGGGCGACTCTGCTGGGACTGTCACTGCTTTCTA
















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|213600429|gb|DB966180.1|DB966180
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|213594204|gb|DB966133.1|DB966133
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|298164262|gb|HO013907.1|HO013907
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|6341392|gb|AW164216.1|AW164216
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|298172564|gb|HO019604.1|HO019604
EST:     TTCCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|209725870|gb|BW654720.1|BW654720
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|192325556|gb|FK019412.1|FK019412
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|7234898|gb|AW570230.1|AW570230
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|192328404|gb|FK020115.1|FK020115
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
EST: gi|13125704|gb|BG316274.1|BG316274
EST:     TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTG                         GTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC
genomic: TTTCATCCATGAAGGAGAACTCCTCAAACTCAAACTTGATAACTATTCTGgtaattaacc ... gacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatcatttgtgtgttattttaagctaaacatgttacctttttgggacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCCTGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA
                      agctaaa  putative branch site (score: 3)
              ttattttaagctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaaccattttctggtttctttgaagacctgtttagtaatgttattgttaacagaccattatctaattttagacaacatttttttttgttagatctggttcttaacggtccatttaataccattgcaacaaatcatttgtgtgttattttaagctaaacatgttacctttttgggacattgcagGTGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGAAAAGTGACCATCCTGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA