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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccaattgtgaataatatatcgaagaacaacatccctgcttattttgcatgttgattaattttcccgtttggccctttaaactttgtctttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAG

Basic information

species Glycine max
transcript GLYMA16G05470.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------------------ccccaattgtgaataatatatcgaagaacaacatccc--tgcttattttgcatg--ttgattaattttcccgt-ttggccctttaaactttgtctttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAG
|| || || | ||| | | | | || | | | || ||| || | | || || | | | | ||| || |||||||||||| |||| |||||||||||||| |||| || ||||| || ||||||||||||| ||||||
gtattgtagcttaaaccttttgttttattgtaaaaaaaaaggaagcttcacctttaagcagaaagattagctgcatgagaccgatggtataaaatttgcaattcgagtttcttacgatgatcaaatgaattgctttggttcaaatggtggtgttaacgactctgattgcacattttat-tcagGTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG

upper sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 4
ccccaattgtgaataatatatcgaagaacaacatccctgcttattttgca---tgttgatta-attttcccgtttggccctttaaactttgtctttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAG
| || || || | | | | | || ||| || ||| || | |||| |||||| || || | || | | | |||| ||||||| || |||||||||| ||| | ||||||||||| |||||||| || |||||||||| ||||||
----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|209716470|gb|BW653884.1|BW653884
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|15814086|gb|BI786361.1|BI786361
EST:     TTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|209711508|gb|BW681444.1|BW681444
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|213602669|gb|DB956605.1|DB956605
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|298191152|gb|HO038631.1|HO038631
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|16105980|gb|BI893720.1|BI893720
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|213620335|gb|DB961480.1|DB961480
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|213587989|gb|DB957448.1|DB957448
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|19452653|gb|BM954063.1|BM954063
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|213602677|gb|DB956613.1|DB956613
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|151393069|gb|EV262944.1|EV262944
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
EST: gi|298194575|gb|HO043047.1|HO043047
EST:     TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAG                         GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC
genomic: TTGTGGATGGTATTCACAGTCAAGTGGCAAAGATTGAGGATGATCTCAAGgtatattcaa ... ttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgttgattaattttcccgtttggccctttaaactttgtctttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAG
         gattaat  putative branch site (score: 3)
 ctttgtctttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccccaattgtgaataatatatcgaagaacaacatccctgcttattttgcatgttgattaattttcccgtttggccctttaaactttgtctttcatgccagGTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
ccccaat
- - - - - - - - - - - - - aacaaca
- - - - - - - - - - - - - - - - - ccctgct
- - - - - - - - - - - - - - - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttta