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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgagctgattagtgttaccatcttcacaaaagaacatgaaaatccttattttgggtggaatggctaacacttgcatcatacttatttgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG

Basic information

species Glycine max
transcript GLYMA20G26580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 5
ttcatgagctgattagtgttaccatcttcacaaaagaacatgaaaatccttatt---ttgggtggaatggctaacacttgcatca-tacttatttgat----tggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG
               |||  |  |||||      ||  ||||| | | |||  |   |    |  | |    |||  |     || |  |  ||||||    ||||||||||||||| || ||||||||||||||||| || ||||| || |  || | |     | | |||| ||| ||  |  | ||||| || || || ||||||
---------------gtgagagaatctt------agtccatgagatttctttgtcgatcatataaactcagaaacgttgttgacagtgttggtttgatgatatggcagGAGAATTGTGGGAGTGGCACATGTTGAGGACTTTGAATCAATCGAAGAAGATAAGCGAAGAGCTATTTGCGAGAGAAGTGCACTCGAGTTTGCGAAGATG

upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 3'ss of exon 5
---ttcatgagctgattagtgttaccat-cttcacaaaagaacatgaaaatccttattttgggtggaatggctaacacttgcatcatacttatttgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG
   |   | ||  |  |  ||  ||| |  |||    |      | | |  | | ||           |   ||| ||||      ||  | || ||||  |||||||||||||||||| ||||||||||||||||| ||||| |||| |||||||   || || ||||  |||||  | | ||||||||  || || ||||||
atttatgtaagtggtatcatgaaaccctgtttcttgcattcttgtcatagacttcatacaattaattttttttaagactt---ctctatct-ttggattcacagGAGAATTGTTGGTGTAGCACATGTTGAGGATTTTGAATCAATTGTTGATGCTAGCAAGCGAGCTAACTGTGAGAGACAGGCACTTGTATTTGCAAAGATG

upper sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 5
ttcatgagctgattagtgttaccatcttcacaaaagaacatgaaa-atccttattttggg--tggaatggctaacacttgcatcatacttat-------ttgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG
          ||||  | | |      |||  ||      ||  | || ||| |  | |   |   |    || | |||   | | ||||||       ||||||  |||||||||||||||||| ||||||||||||||||| ||||| |||| |||||||   || || ||||  |||||  | | ||||||||  || || ||||||
---------cgatttatataagtggtatcatgaagccctgtgttacattcttgtcatagacttcatacaattatctctttt-taagacttatcgatcttttgattcacagGAGAATTGTTGGTGTAGCACATGTTGAGGATTTTGAATCAATTGTTGATGCTAGCAAGCGAGCTAACTGTGAGAGACAGGCACTTGTATTTGCAAAGATG

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|6228208|gb|AW156807.1|AW156807
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|151395006|gb|EV264877.1|EV264877
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|9987542|gb|BE661650.1|BE661650
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|8286458|gb|BE024026.1|BE024026
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|16342269|gb|BI967864.1|BI967864
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|6072956|gb|AW102343.1|AW102343
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|254322009|gb|GR837423.1|GR837423
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|209713484|gb|BW679274.1|BW679274
EST:     TGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: TGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|151395015|gb|EV264886.1|EV264886
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|254332676|gb|GR844046.1|GR844046
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTG-TGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
EST: gi|209710607|gb|BW676533.1|BW676533
EST:     ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAG                         GAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC
genomic: ACAGATTTGTTTCACGACAGTCTTGGATTTGGTGCTGCTAAAATGATTAGgtgagacttt ... tgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccttattttgggtggaatggctaacacttgcatcatacttatttgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG
                                       cttattt  CT-rich tract
                                    atacttatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgagctgattagtgttaccatcttcacaaaagaacatgaaaatccttattttgggtggaatggctaacacttgcatcatacttatttgattggcagGAGAATTGTTGGTGTGGCACATGTTGAGGATTTCGAATCCATTGCTGATGCTGCTAAACGGGCTAGTTGTGAACGGCGGGCACTTGATTTAGCTAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tcatgag
- - - - - - - - tgttacc
- - - - - - - - - - - - tcttcac
- - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatc