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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaacttgttaaagctgggctgctattacttactaatttaaagtttggtcttatattgatgaatgaccaaataacttgtctgatcaccagctgtgattaaaacaatagactgatgagaaataagtttcttttgtcctatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAATACAGATGAGCTTGTAACCTCTCCCAACAAAGATGGCCATGTCAACAATT

Basic information

species Glycine max
transcript GLYMA20G33190.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtgaacttgttaaagctgggctgctattacttactaatttaaagtttggtcttatattgatgaatgaccaaataacttgtctgatcacca-gctgtgattaaaacaatagactgatgagaaataagtttcttttgtcctatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAATACAGATGAGCTTGTAACCTCTCCCAACAAAGATGGCCATGTCAACAATT
                                        |||   | ||||     ||||| |||     | | | |   ||| |   || || |||||  | ||| | | ||      ||||      ||    || |  |  ||| |||||||||| ||| ||||| ||||||||||||||||| |||||||| || ||   | |||||| ||| |   | ||||||||||||||||||||||||||||
----------------------------------------attcctactttgaa---atattcatg--cagcaacagagtatgtttacgcatcatgctgtt-tcaaagccaaag------gagaccatgattctaattcttgttattaacagGAAGGACACTACGAGTATAAGTACATTGTTGATGGCGAATGGACGTGTAACGAACATGAGCATGTTAGAGCCCCCAACAAAGATGGCCATGTCAACAATT
















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|13481870|gb|BG511213.1|BG511213
EST:     TAAATTTTGATGACAAAGAGGGTTTGTGGTTTCTCAAGAGGGAATTGCCT                         GAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAAT
genomic: TAAATTTTGATGACAAAGAGGGTTTGTGGTTTCTCAAGAGGGAATTGCCTgtaagtgaac ... tatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAAT
EST: gi|193591625|gb|FK548672.1|FK548672
EST:     AAATTTTGATGACAAAGAGGGTTTGTGGTTTCTCAAGAGGGAATTGCCT                         GAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAAT
genomic: AAATTTTGATGACAAAGAGGGTTTGTGGTTTCTCAAGAGGGAATTGCCTgtaagtgaac ... tatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAAT
EST: gi|192321002|gb|FK013504.1|FK013504
EST:     TAAATTTTGATGACAAAGAGGGTTTGTGGTTTCTCAAGAGGGAATTGCCT                         GAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAAT
genomic: TAAATTTTGATGACAAAGAGGGTTTGTGGTTTCTCAAGAGGGAATTGCCTgtaagtgaac ... tatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgattaaaacaatagactgatgagaaataagtttcttttgtcctatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAATACAGATGAGCTTGTAACCTCTCCCAACAAAGATGGCCATGTCAACAATT
                gactgat  putative branch site (score: 3)
                                 tttcttttgtcctatt  putative PPT
                          aaataagtttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaacttgttaaagctgggctgctattacttactaatttaaagtttggtcttatattgatgaatgaccaaataacttgtctgatcaccagctgtgattaaaacaatagactgatgagaaataagtttcttttgtcctatttaccagGAAGGACTCTATGAGTACAAGTACATTGTTGATGGGGAATGGACATGCAATACAGATGAGCTTGTAACCTCTCCCAACAAAGATGGCCATGTCAACAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG