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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttttctgaataatctattgaagaacaacatccctgcttattttgcatgttgattaattttcccatttggccctttaaactttgtcttccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAG

Basic information

species Glycine max
transcript GLYMA19G27360.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------tttgttttctgaa--taatctattgaagaacaacatccctgcttattttg-----catgttgattaattt--tcccatttggccctttaa--actttgtcttc-catgc----cagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAG
                                                                  || | |   |||     ||    | ||       || |  | || ||  |     ||  |  |||  |||  | | | | |     ||||  ||| ||  | | |||      |||||||||||| |||| ||||||||||||||  |||| || ||||| || |||||||||||||  |||||
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttattcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG

upper sequence: GLYMA19G27360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 4
tttgttttctgaataatctattgaagaacaacatccctgcttattttgca---tgttgatta-attttcccatttggccctttaaactttgtcttccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAG
    |    | || ||  |  |  | |      | | |  ||  ||| ||   ||| || |  ||||     |||||   || || | || | |   |||| |||||||  || |||||||||| ||| | ||||||||||| |||||||| || ||||||||||  |||||
----tgagataaaaaaaattgtatacatatttttacttatttggtttacagtttgtagactgtatttggatgtttgggtattgaatcattatttcttatgctagGTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG
















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|10846063|gb|BF069052.1|BF069052
EST:     TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAGgtattcattt ... tccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|192300408|gb|FG988825.1|FG988825
EST:     TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAGgtattcattt ... tccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|7478459|gb|AW666273.1|AW666273
EST:     TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAG                         GTTCGTGTNTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAGgtattcattt ... tccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|7693148|gb|AW761245.1|AW761245
EST:     TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAGgtattcattt ... tccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|298194875|gb|HO043347.1|HO043347
EST:     TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TCGTGGATGGTATTCACAGTCAAGTGGCAAAGATCGAGGATGATCTCAAGgtattcattt ... tccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgttgattaattttcccatttggccctttaaactttgtcttccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAG
         gattaat  putative branch site (score: 3)
                                     ctttgtcttcc  putative PPT
     tgttgattaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttttctgaataatctattgaagaacaacatccctgcttattttgcatgttgattaattttcccatttggccctttaaactttgtcttccatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - aacaaca
- - - - - - - - - - - - - - - - - ccctgct
- - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttta