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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatataactaactgatttccttttatgattgtgttaagaaaccatctgaactgatacttacaaatttttttaaggaacgttttatgatatatattttggtctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAATACATCACTGCTGCTGCTTAATTATCCATTCTTAGGCCAATGCCTTCTA

Basic information

species Glycine max
transcript GLYMA15G42140.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 13
-------gttatataactaa---ctgatttccttttatgattgtgttaagaaacc-----atctgaactgatacttacaaatttttttaaggaacgttttatgatatatattttggtctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAATACATCACTGCTGCTGCTTAATTAT-CCATTCTTAGGCCAATGCCTTCTA
        |||| || ||||   || |    | | | | |  ||   || || ||     || ||   | || |   ||||||  ||    |||  |  | |  | | ||| |  ||   ||||||||||||||||||||||||||| |||||||| |||||||||||||||||  | | ||||  ||||||||| ||| | | |||    | |   ||   ||    
gtatatctttatttatctaaaatctcagaatcatctgttagggttaaaacaaccctcatgatgtgggataattccatcaaattacttctctgaaaatcgtttc-tgtttatat--gttcttttacagGTTTATGGACCTGAGGCAACCATGACTGGCATATGCAAACAGGCAATTGAGTGCATCGGTGCTGCTGCATAAGTGTACCAAATCTTGATAAAAATCTCTG-
















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|31471041|gb|CD413069.1|CD413069
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|14991230|gb|BI316903.1|BI316903
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|7924163|gb|AW830189.1|AW830189
EST:     TCTATCAAAAATGAGGGCACCTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTTTATGCAAACAGGCAATCCAA
genomic: TCTAGCAAAAATGAGGGCAC-TCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|6502280|gb|AW203653.1|AW203653
EST:     GTCTAGCAAAAATGAAGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|6726078|gb|AW310477.1|AW310477
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|58022555|gb|CX709296.1|CX709296
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|192330363|gb|FK021164.1|FK021164
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|31465942|gb|CD407970.1|CD407970
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|213598090|gb|DB977660.1|DB977660
EST:     AGAGGAAATTGGCATTCCTATTGAG                         GTTTATGAACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: AGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
EST: gi|10253168|gb|BE820934.1|BE820934
EST:     GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAG                         GTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA
genomic: GTCTAGCAAAAATGAGGGCACTCGGAGAGGAAATTGGCATTCCTATTGAGgttatataac ... ctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttacaaatttttttaaggaacgttttatgatatatattttggtctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAATACATCACTGCTGCTGCTTAATTATCCATTCTTAGGCCAATGCCTTCTA
                                            tctctttac  CT-rich tract
      aaatttttttaaggaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatataactaactgatttccttttatgattgtgttaagaaaccatctgaactgatacttacaaatttttttaaggaacgttttatgatatatattttggtctctttacagGTTTATGGACCTGAGGCAACAATGACTGGTATATGCAAACAGGCAATCCAATACATCACTGCTGCTGCTTAATTATCCATTCTTAGGCCAATGCCTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT