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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctctattctttctactggtgcaaatgagagtgttacctgtataaagtaaatattctaaccaattgaaaaaaattttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA

Basic information

species Glycine max
transcript GLYMA08G21370.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g44922.1 (Oryza sativa), 3'ss of exon 12
gtgagctctattctttctactggtgcaaatgagagtgttacctgtataa-----agtaaatattctaaccaattgaaaaaa-----attttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA
|| | || | ||   |  ||    |   || ||  ||||||   | | |      ||   |||| ||   | |||  ||       ||| |   |   |||||| |||||||||||||||||| ||||||| | |||||| || ||||| || ||||| || || || || |||||| |||||||||||||||| || ||
gtaa-ctatgtttgcttcacacagg---ataaggttgttacacatcttattactggtctctattgtactaagttgtgaagttccctattattatttgcagATCCTACCTACATGATCCGAGCTATTCCAAGCAATGCATCAGACAATGTCTACTGCACGCTGCTGGCCCACAGTGCTATTCATGGTGCAATGGCCGGCTA

upper sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
----------------------------------------------gtgagctctat-tctttctactggtgcaaatgagagtgt-tacctgtataaagtaaatattctaaccaattgaaaaaaattttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA
                                              |  || |  |  |  | ||  |  |    ||  |||| | | ||| |  || ||    ||   | ||  ||       ||||    ||  |||||| |||||||||||||| ||  ||||||| | |||||| || ||||| || ||||| || || || || |||||  ||||||| ||||||||||||||
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaagtactactttttatatgtatctgagtatctccctatggaatgttgcaataacagcctgtt-------atttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtgagctctattctttctact-ggtgca---aatgagagt--gttacctgtataaagt-aaatattctaaccaattgaaaaaaattttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA
|| | |    |  ||| |||| |||| |   | ||  |||  || |  | ||  | || ||  | ||| |  || ||      ||||| |    ||||||| || ||||||||||| ||| ||||||| | |||||| || ||||| |||||||| || || || || |||||  |||||||||||||||| |||||
gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatctgatgaagtgcctgccatttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
----gtgag-ctctattctttctactggtgcaaatgagagtgttacct-gtataaagtaaatattctaacca-attgaaaaaaat---tttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA
       || | ||| | ||  |   ||      | |  |||     | |||    | ||     || | || | | | |    |   |  || ||  |||||| || |||||||| |||||||| || |||||||||||||||||||| || |||||  |  | || || |||||  | |||||||| |||||||| | 
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT

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|209712326|gb|BW671176.1|BW671176
EST:     GACCACTTCACAAAAAGTCGAAAGATGGATATAACTCTGAAGTACATTG                         ATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTAT
genomic: GACCACTTCACAAAAAGTCGAAAGATGGATATAACTCTGAAGTACATTGgtgagctcta ... tgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTAT
EST: gi|209712325|gb|BW671175.1|BW671175
EST:     GACCACTTCACAAAAAGTCGAAAGATGGATATAACTCTGAAGTACATTG                         ATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTAT
genomic: GACCACTTCACAAAAAGTCGAAAGATGGATATAACTCTGAAGTACATTGgtgagctcta ... tgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttacctgtataaagtaaatattctaaccaattgaaaaaaattttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA
                      ttctaac  putative branch site (score: 1)
         tataaagtaaatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctctattctttctactggtgcaaatgagagtgttacctgtataaagtaaatattctaaccaattgaaaaaaattttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA