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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcctctatctttttatttctttgtatttgtgtcattcctcaaggttgaggtgagtctttttttcaaagtgactaattggtaactgtaaaatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTTGTTAGAGGTCAAAAGCATTTGTTGAAGAATATACGTAGAAGGAAACATC

Basic information

species Glycine max
transcript GLYMA08G05220.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G05220.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g05970.t01 (Vitis vinifera), 3'ss of exon 1
---gtgcctctatctttttatttctttgtatttgtgtcattcctcaaggttgaggtgagtctttttttcaaagtgactaattggtaactgtaaaatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTTGTTAGAGGTCAAAAGCATTTGTTGAAGAATATACGTAGAAGGAAACATC
        |||  |  |  ||  ||  ||   | |||  |||||      |   | ||| ||| | |   ||    | | | | ||| | |    | |  ||||||||||| ||||||||||| |||  |||||||||||| |||||    ||  | ||||||||||||||||| || |||||||| ||| |||||||||| |
atgaattttctcccaatccatagctgagtcactttgtatttcct--gctctagtgagagccttatatgtgaaact-caattcgttaattctcctttgtttcagGGTTTCAGAAAAATTGATACAGATCACTGGGAATTTGCAAATGAAGGATTCATCAGAGGTCAAAAGCATTTATTAAAGAATATCCGTCGAAGGAAACAAC
















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|213606436|gb|DB963001.1|DB963001
EST:     ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTAT                         GGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
EST: gi|213593151|gb|DB969893.1|DB969893
EST:     ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTAT                         GGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
EST: gi|209712081|gb|BW676697.1|BW676697
EST:     ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTAT                         GGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
EST: gi|19348840|gb|BM893372.1|BM893372
EST:     ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTAT                         GGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
EST: gi|209712405|gb|BW671257.1|BW671257
EST:     ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTAT                         GGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
EST: gi|192299005|gb|FG990361.1|FG990361
EST:     ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTAT                         GGTTTGAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: ATTTCAAACACAACAATTTCTCCAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
EST: gi|254317228|gb|GR826173.1|GR826173
EST:     CAGTTTCATCAGACAACTCAATATCTAT                         GGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT
genomic: CAGTTTCATCAGACAACTCAATATCTATgtccgtctct ... aatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaggtgagtctttttttcaaagtgactaattggtaactgtaaaatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTTGTTAGAGGTCAAAAGCATTTGTTGAAGAATATACGTAGAAGGAAACATC
                                 tggtaac  putative branch site (score: 2)
             tttttttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctctatctttttatttctttgtatttgtgtcattcctcaaggttgaggtgagtctttttttcaaagtgactaattggtaactgtaaaatctaacagGGTTTCAGGAAAATTGATACGGATTGCTGGGAATTTGCCAATGAGAACTTTGTTAGAGGTCAAAAGCATTTGTTGAAGAATATACGTAGAAGGAAACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA