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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagattgtttggtattggctgttttgcatatcagatcacttttgcatcccaagtgtgttcagttctccctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA

Basic information

species Glycine max
transcript GLYMA12G33520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
tagattgtttggtattggctgttttgcat--atcagatcacttttgcatcccaagtgtgttcagttctccctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
              | || | | |||  |   |   | || || ||  || |  || | ||      |   ||     |  |   |||  | | ||   ||||||||||| || ||||| ||||| || |||||||||||||| ||||||  |||||| || || ||||||||||| ||||| ||||| |||||||| || |
-------------gtaggttatcttgtttttgtttaagca-ttatgtgtctctggtttattagaagttgtgtg-----taatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA

upper sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 5
tagattgtttggtattggctgttttgcatatcagatcacttttgcatcccaagtgtgttcagttctc--cctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
      || | | |||||   | |||  |   |    | |           ||||  ||  |       | | | || | ||  |||||||    ||  ||||||||||| |||||||| || || || || ||||| ||||| |||||||  || || ||||| ||||| ||||| ||||| || || ||||||||||| |
------gtatagcattggtgatcttgattgcaaatctaatgacatgagattagtggttttggcctgaagcattagctctttt-tgaatctt----tgtgcagGGAGAAGCTAAAAGTGCTCAGCTTATCGGACAAGCAATTGCGAACAATCAGGCATTCATCACTCTGAGAAAGATTGAAGCTGCGAGAGAGATTGCACAGA

upper sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 3'ss of exon 5
tagattgtttggtattggctgttttgcatatcagatcact-tttgcatcccaagtgtgttcagttctccctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
          |  |   | |  | | ||| ||   |     | |  |  |  || | |   | |  |   ||||     || |  ||   |   ||   |||||||||| || ||||| || || ||||| ||||| ||||| ||||| | ||| |||||||| || |||||||| || || ||||| ||||||||||| |
----------gtaaagagattctctacatttccacttgtaatctaaactctgagagcgaa-attgttgtgtgacgaaagtt-cacatggct---tgtgtagGGAGAAGCCAAGAGTGCTCAGCTCATTGGTCAAGCAATTGCAAACAACCAAGCGTTTATCACGCTCAGGAAGATCGAGGCTGCAAGAGAGATTGCACAGA

upper sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
tagattgtttggtattggct-gttttgcatatcagatcacttttgcatcccaagtgtgttcagttctccctgacctttctta--cgaatcttt-taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
   | | |    || | | | | |||| |   | |||      ||  || |   | | |||||||          |    ||  | ||||| | |  ||| ||||| || || || |||||||| ||||| || ||||||||||||||||||||||| || ||||| || || || || |||||  |  | || ||||||||||
---aatttcaaatactagtttgatttggacccctgattgagggtggttcacct-tcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

upper sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 6
tagattgtttggtattggctgttttgcatatcagat-cacttttgcatc---ccaagtgtgttcagttctccctgacctttctta--cgaatct---tttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
        |||    ||| |    | | | | || | ||||     ||    ||   | | ||||||| ||    |  ||   ||  | |||||   | |  ||| ||||| || || || |||||||| ||||| || ||||||||||||||||||||||| || ||||| || || || || |||||  |  | || ||||||||||
--------ttgagggtggttcaccttcctcttagttacactcaaatattgtgccccttcttttcagtt-tcataaattttaagtaagcaaatctgtctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

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|4260371|gb|AI416867.1|AI416867
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgatgataa ... taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
EST: gi|192329319|gb|FK020238.1|FK020238
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgatgataa ... taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
EST: gi|17401769|gb|BM178551.1|BM178551
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgatgataa ... taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
EST: gi|192303430|gb|FG997460.1|FG997460
EST:     TTGTGGAAAAAGCTGAGCAAGACAGGAGAAGTGCTGTAATTAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgatgataa ... taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
EST: gi|8401623|gb|BE057257.1|BE057257
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATTAGAGCACAGgtgatgataa ... taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccaagtgtgttcagttctccctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA
                                        tctttt  CT-rich tract
                                      aatcttttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagattgtttggtattggctgttttgcatatcagatcacttttgcatcccaagtgtgttcagttctccctgacctttcttacgaatcttttaatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - ttgtttg
- - - - - - - -tggctgt
- - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - -gcatccc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttc