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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaataaaacacatcttctactgttttctctttctaagcattttcttcaagacaatgaagacatattgataattaacacgaggcatacgtcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGGGCAAATTGGATTCAAGGGAAGGACTGAAGAGTACTTTTGAATTCCAAAC

Basic information

species Glycine max
transcript GLYMA12G09730.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09730.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g00920.t01 (Vitis vinifera), 3'ss of exon 3
atgaataaaacacatcttctactgttttctctttctaagcattttcttcaagacaatgaagac-atattgataattaacacgaggcatacgtcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGGGCAAATTGGATTCAAGGGAAGGACTGAAGAGTACTTTTGAATTCCAAAC
 |   |     |    ||  |    |  ||  |   |   || || |  | |    | |     || ||  |||||    | |  | |   | ||   |||||| ||| |||| || |||||||||||  | ||| ||||||| ||||||||||||||||| |||||||| |||||||| || |||||||||        |
cttcttgtttgatccattgcatccataccttatctaacatatGTTGTGGATGGTTTTTACTTTTATTTTTTTAATTTTTTCAAAACTTGAAT-ATCAACAGGTTGTGGATGGTCACATGGCACCTTGGTCTATTCCTCTGCCTTACTTTTGGGCAAATTGGGTTCAAGGGCAGGACTGAGGATTACTTTTGAGAAGATCTC
















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|31458119|gb|CD400147.1|CD400147
EST:     GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
EST: gi|13481666|gb|BG511009.1|BG511009
EST:     GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
EST: gi|22931458|gb|BU548597.1|BU548597
EST:     GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
EST: gi|6482824|gb|AW202036.1|AW202036
EST:     GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
EST: gi|10844463|gb|BF067734.1|BF067734
EST:     GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
EST: gi|208144764|gb|GD943089.1|GD943089
EST:     GCTGAGCTTGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTT
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTT
EST: gi|31307026|gb|CD392229.1|CD392229
EST:     GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTG                         GTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG
genomic: GCTGAGCTAGCTCACTTCCCCACCCCTCCTGCCCTTACTTCATCCTTTTGgttagtcact ... tcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaagacaatgaagacatattgataattaacacgaggcatacgtcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGGGCAAATTGGATTCAAGGGAAGGACTGAAGAGTACTTTTGAATTCCAAAC
                          aattaac  putative branch site (score: 2)
                acatattgataattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaataaaacacatcttctactgttttctctttctaagcattttcttcaagacaatgaagacatattgataattaacacgaggcatacgtcatgcgcagGTTATGGCTGGTTACGTGGCACCTTGGCTTGTTCATCTGCCTCACTTTTGGGCAAATTGGATTCAAGGGAAGGACTGAAGAGTACTTTTGAATTCCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - aacacat
- - - - - - - - -tctactg
- - - - - - - - - - - - - - - - - ctaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatacg