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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcactcctctctctctctctctctctctttagttagctagggtttcatttctctagaaaaccgcttctatttttacatgtttttatgtacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTAATGCGAGTCATTGATG

Basic information

species Glycine max
transcript GLYMA10G02690.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 2
--------------------gtatgtcactcctctctctctctctctctctctttagttagctagggtttcatttctctagaaaaccgcttctatttttacatgtttttatgtacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTAATGCGAGTCATTGATG
                      |  | ||| ||   | |    ||      || |     || |  || | | |  ||| ||| |    ||     ||| |||||  ||   |  |   |||||||||||||||||||||||  ||||||||||||||| | ||||||||| ||||||  | ||||||||||||||||||||  |||| ||  |||||||| 
gtaaggaaaaagaaccttcatcaaatgacttcttattgttatgcttgtatactgtctaatgcaaaagtataagtgttcttgaagaa-attttgggatttccatgtgctt---tgtagatcagAAGGATGAGTCTTTTTACACTTTGAGTTGGGCATGCAGTATTGATGGCATCCCATTCTTGGTGGCTGGAGGAATCAATGGTATAATTCGTATCATTGATA
















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|15815907|gb|BI788182.1|BI788182
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         AAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|192318898|gb|FK008026.1|FK008026
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         AAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|192313911|gb|FK007671.1|FK007671
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         AAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|298172647|gb|HO019687.1|HO019687
EST:     GTCTCGAAGGAGGAGTTATTACTGCTTTGCAATCTTATGTAGACGAAGAT                         AAGGGTGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|192318897|gb|FK008025.1|FK008025
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         AAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|151412933|gb|EV282745.1|EV282745
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         --G-ATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|298189755|gb|HO038158.1|HO038158
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         AAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
EST: gi|192313912|gb|FK007672.1|FK007672
EST:     GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGAT                         AAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC
genomic: GTCTCGAAGGAGGAGTTATTGCTGTTTTGCAATCTTATGTAGACGAAGATgtatgtcact ... tacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatttctctagaaaaccgcttctatttttacatgtttttatgtacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTAATGCGAGTCATTGATG
                      ttctatttttacatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcactcctctctctctctctctctctctttagttagctagggtttcatttctctagaaaaccgcttctatttttacatgtttttatgtacacgccagAAGGATGAGTCTTTTTACACAGTGAGTTGGGCATGCAATGTTGATGGCACCCCATTTGTTGTGGCTGGAGGAATCAATGGGGTAATGCGAGTCATTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA