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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcagctcttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

Basic information

species Glycine max
transcript GLYMA15G10470.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
--attctccccttgtggaattttttgggctatcca---agataattgtgttatattacagcttc-----tattcgtatagaacagtgttaatgtt-cagctcttac------------tgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
  ||   |   || | |  |  |||  | |   ||       | |||  | ||    ||   ||      || |   ||||||| ||||||  |  ||||||   |            |||||| | || | || || |||||| ||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || ||||||||||||| |||| 
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
--attctccccttgtggaattttttgggctatccaag-ataattgtgttatattacagct---tctattcgtatagaacagtgttaatgtt-cagctcttac------------tgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
    | |    | |  || ||   | |   ||      ||     || |     |||         || |   ||||||| ||||||  |  ||||||   |            |||||| | || | || || |||||| ||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || ||||||||||||| |||| 
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcagctct-tactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC------
  ||||   |  |  | | |        ||  |         | |  || |  |  || |     | |     | |  |    || |  | | |  | |||| | |  |  |  | |||||| ||||||| || ||||||||||| |||||||||||||| || || ||||| ||  |        |||||| |||| ||       
ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaatgtaaattttgca-atgtctctaatttgtcccatttatttatatcttacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGT------CTCTTTGGTTTCTACAAATCACA

upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 6
-attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcag-ctcttact----gcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
    |    |   |        |  |||| |      | | | |   || |||  ||||    |  ||  ||| | ||    |    |  |||||| |    |||||| |||||  |||| || ||| ||||||| ||||| || |||||||||||||||||||| || || ||||||| |   ||  ||||  | || || |   
gtgccatagcccataagtaaactcaggctgtttg---tcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagCAGAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCT---

upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156251_T02 (Zea mays), 3'ss of exon 6
attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcag-ctcttact----gcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
   |    |   |        |  |||| |      | | | |   || |||  ||||    |  ||  ||| | ||    |    |  |||||| |    |||||| |||||  |||| || ||| ||||||| ||||| || |||||||||||||||||||| || || ||||||| |   ||  ||||  | || || |  |
--ccatagcccataagtaaactcaggctgtttg---tcactttcaaatgttattgcttaatatgatactgaatattgaggtttccaaatctcttattaacagcagAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCTATC

upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
-attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcagct---cttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
 | |||   |        |      ||    |||     | |    || |  | |  ||  | |      ||   ||| ||||  |    |   |||| | |||| | || || | || || ||| ||||||||||||||||||| || ||||| ||||| || || |||||||| ||  | ||    || |||| | ||||| 
gagtcttatcagccatggtccaaaaggaagcccat----actaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA

upper sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
attctccccttgtggaattttttgg----gctatccaagataattgtgttatattacagcttctattcgtatagaacagtgtta-atgttcagctcttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
  | ||  | |||||     | |      | |   |||| |  || || ||  ||  || || ||    |  |   | || ||| || | ||  ||| |   ||||| ||||| || || || ||| ||||||| |||||||||||||| ||||||||||| || ||||| |||||| | || ||||| || |||||||||||||
--tttcatcatgtggctccatataattttgttgatcaagttggttctgatac-ttgtagtttgtagattttgattgctgtcttatatctccatttctaa--acagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC

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|26056174|gb|CA799088.1|CA799088
EST:     GGGGAATTGCAGTTCCAGAGGCCAATGCCGAACTGCAAGCAAATATTGAT                         AGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTT
genomic: GGGGAATTGCAGTTCCAGAGGCCAATGCCGAACTGCAAGCAAATATTGATgtatgtctga ... cttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTT
EST: gi|51341621|gb|CO982938.1|CO982938
EST:     GGGGAATTGCAGTTCCAGAGGCCAATGCCGAACTGCAAGCAAATATTGAT                         AGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTT
genomic: GGGGAATTGCAGTTCCAGAGGCCAATGCCGAACTGCAAGCAAATATTGATgtatgtctga ... cttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattacagcttctattcgtatagaacagtgttaatgttcagctcttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC
                                           ctcttac  putative branch site (score: 3)
                                           ctcttact  CT-rich tract
                                ttaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcagctcttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- -ctcccct